6FT6 | pdb_00006ft6

Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
C [auth B]SCOP2B SuperfamilyTranslational proteins 8078363 3000811 SCOP2B (2022-06-29)
D [auth C]SCOP2B Superfamily60S ribosomal protein L4 C-terminal domain-like 8052815 3002143 SCOP2B (2022-06-29)
D [auth C]SCOP2B SuperfamilyRibosomal protein L4 8052816 3001146 SCOP2B (2022-06-29)
E [auth D]SCOP2B SuperfamilyTranslational machinery components 8052875 3000571 SCOP2B (2022-06-29)
F [auth E]SCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain 8053109 3000334 SCOP2B (2022-06-29)
G [auth F]SCOP2B SuperfamilyRibosomal protein L30p/L7e 8052917 3001378 SCOP2B (2022-06-29)
G [auth F]SCOP2B SuperfamilyRibosomal L30p/L7e protein, N-terminal domain-lke 8052916 3002152 SCOP2B (2022-06-29)
H [auth G]SCOP2B SuperfamilyL30e-like 8063962 3001739 SCOP2B (2022-06-29)
K [auth J]SCOP2B SuperfamilyRL5-like 8073884 3001709 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRibosomal protein L13e-like 8053159 3002162 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyRibosomal proteins S24e, L23 and L15e 8082481 3000210 SCOP2B (2022-06-29)
OSCOP2B SuperfamilyRibosomal protein L13 8066053 3001134 SCOP2B (2022-06-29)
PSCOP2B SuperfamilyRibosomal protein L22 8076708 3001078 SCOP2B (2022-06-29)
QSCOP2B SuperfamilyRibosomal proteins L15p and L18e 8095970 3001045 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyRibosomal protein L19 (L19e) 8077485 3000890 SCOP2B (2022-06-29)
USCOP2B Superfamily60S Ribosomal protein L22e 8053058 3002158 SCOP2B (2022-06-29)
VSCOP2B Superfamily50S Ribosomal protein L14-like 8103364 3000433 SCOP2B (2022-06-29)
XSCOP2B SuperfamilyRibosomal proteins S24e, L23 and L15e 8095962 3000210 SCOP2B (2022-06-29)
YSCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain 8076760 3000334 SCOP2B (2022-06-29)
ZSCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain 8053046 3000334 SCOP2B (2022-06-29)
FA [auth f]SCOP2B SuperfamilyTranslational proteins 8087451 3000811 SCOP2B (2022-06-29)
GA [auth g]SCOP2B SuperfamilyRibosomal protein L34e-like 8053547 3002203 SCOP2B (2022-06-29)
IA [auth i]SCOP2B SuperfamilyRibosomal protein L36e 8053115 3002161 SCOP2B (2022-06-29)
JA [auth j]SCOP2B SuperfamilyZn-binding ribosomal proteins 8080044 3001320 SCOP2B (2022-06-29)
KA [auth k]SCOP2B SuperfamilyRibosomal L38e protein-like 8053562 3002206 SCOP2B (2022-06-29)
LA [auth l]SCOP2B SuperfamilyRibosomal protein L39e 8078549 3001756 SCOP2B (2022-06-29)
OA [auth p]SCOP2B SuperfamilyZn-binding ribosomal proteins 8103126 3001320 SCOP2B (2022-06-29)
SA [auth v]SCOP2B SuperfamilyClass II aaRS ABD-related 8092352 3000465 SCOP2B (2022-06-29)
SA [auth v]SCOP2B SuperfamilyClass II aaRS ABD-related 8092351 3000465 SCOP2B (2022-06-29)
TA [auth w]SCOP2B SuperfamilyRrs1-like 8092359 3002595 SCOP2B (2022-06-29)
VA [auth y]SCOP2B SuperfamilyPentein 8036230 3000640 SCOP2B (2022-06-29)
BB [auth KK]SCOP2B SuperfamilyRrp6-Rrp47 interacting regions-like 8055988 3002328 SCOP2B (2022-06-29)
CB [auth LL]SCOP2B SuperfamilyRrp6-Rrp47 interacting regions-like 8055987 3002328 SCOP2B (2022-06-29)
CA [auth c]SCOP2B SuperfamilyL30e-like 8039862 3001739 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
B [auth A]V-sete6ft6A1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
C [auth B]V-sete6ft6B1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
D [auth C]V-sete6ft6C2 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
D [auth C]Ald_deCOasee6ft6C3 A: a/b three-layered sandwichesX: Rubredoxin-likeH: Ferritin/Heme oxygenaseT: Heme oxygenase/Ribonucleotide reductaseF: Ald_deCOaseECOD (v294.1)
E [auth D]V-sete6ft6D1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
F [auth E]V-sete6ft6E1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
G [auth F]V-sete6ft6F1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
H [auth G]V-sete6ft6G1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
I [auth H]V-sete6ft6H1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
J [auth I]V-sete6ft6I1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
K [auth J]V-sete6ft6J1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
LV-sete6ft6L1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
MV-sete6ft6M1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
NV-sete6ft6N1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
OV-sete6ft6O1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
PV-sete6ft6P1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
QV-sete6ft6Q1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
RV-sete6ft6R1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
SV-sete6ft6S1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
TV-sete6ft6T1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
UV-sete6ft6U1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
VV-sete6ft6V1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
XV-sete6ft6X1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
YV-sete6ft6Y1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
ZV-sete6ft6Z1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
AA [auth a]Amino_oxidasee6ft6a1 A: a/b three-layered sandwichesX: Phosphorylase/hydrolase-likeH: Peptidyl-tRNA hydrolase-likeT: Peptidyl-tRNA hydrolase-likeF: Amino_oxidaseECOD (v294.1)
DA [auth d]V-sete6ft6d1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
EA [auth e]V-sete6ft6e1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
FA [auth f]V-sete6ft6f1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
GA [auth g]V-sete6ft6g1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
HA [auth h]V-sete6ft6h1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
IA [auth i]V-sete6ft6i1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
JA [auth j]V-sete6ft6j1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
KA [auth k]V-sete6ft6k1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
LA [auth l]V-sete6ft6l1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
OA [auth p]V-sete6ft6p1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
UA [auth x]V-sete6ft6x1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
VA [auth y]V-sete6ft6y1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
BB [auth KK]V-sete6ft6KK1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
CB [auth LL]V-sete6ft6LL1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
DB [auth MM]V-sete6ft6MM1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
CA [auth c]V-sete6ft6c1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)
WV-sete6ft6W1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: V-setECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B [auth A]PF03947Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C)Ribosomal Proteins L2, C-terminal domainDomain
B [auth A]PF00828Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A)Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27AThis family includes higher eukaryotic ribosomal 60S L27A, archaeal 50S L18e, prokaryotic 50S L15, fungal mitochondrial L10, plant L27A, mitochondrial L15 and chloroplast L18-3 proteins. Domain
C [auth B]PF06858Nucleolar GTP-binding protein 1 (NOG1) (NOG1)Nucleolar GTP-binding protein 1 (NOG1)- Family
C [auth B]PF17835NOG1 N-terminal helical domain (NOG1_N)NOG1 N-terminal helical domainThis domain is found at the N-terminus of NOG1 GTPase proteins. Domain
D [auth C]PF1437460S ribosomal protein L4 C-terminal domain (Ribos_L4_asso_C)60S ribosomal protein L4 C-terminal domainThis family is found at the very C-terminal of 60 ribosomal L4 proteins. Domain
D [auth C]PF00573Ribosomal protein L4/L1 family (Ribosomal_L4)Ribosomal protein L4/L1 family- Family
E [auth D]PF17144Ribosomal large subunit proteins 60S L5, and 50S L18 (Ribosomal_L5e)Ribosomal large subunit proteins 60S L5, and 50S L18- Family
E [auth D]PF01198Ribosomal protein L31e (Ribosomal_L31e)Ribosomal protein L31e- Family
E [auth D]PF14204Ribosomal L18 C-terminal region (Ribosomal_L18_c)Ribosomal L18 C-terminal regionThis domain is the C-terminal end of ribosomal L18/L5 proteins. Domain
F [auth E]PF01655Ribosomal protein L32 (Ribosomal_L32e)Ribosomal protein L32- Family
F [auth E]PF01159Ribosomal protein L6e (Ribosomal_L6e)Ribosomal protein L6e- Family
G [auth F]PF00327Ribosomal protein L30p/L7e (Ribosomal_L30)Ribosomal protein L30p/L7eThis family includes prokaryotic L30 and eukaryotic L7. Domain
G [auth F]PF01247Ribosomal protein L35Ae (Ribosomal_L35Ae)Ribosomal protein L35AeThis entry represents the ribosomal eL33 previously known as L35A, eukaryotic and archaebacterial ribosomal proteins. Domain
H [auth G]PF01248Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae)Ribosomal protein L7Ae/L30e/S12e/Gadd45 familyThis family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ...This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118 [1].
Domain
I [auth H]PF00831Ribosomal L29 protein (Ribosomal_L29)Ribosomal L29 protein- Family
I [auth H]PF00347Ribosomal protein L6 (Ribosomal_L6)Ribosomal protein L6Domain
J [auth I]PF12171Zinc-finger double-stranded RNA-binding (zf-C2H2_jaz)Zinc-finger double-stranded RNA-binding- Family
J [auth I]PF01158Ribosomal protein L36e (Ribosomal_L36e)Ribosomal protein L36e- Family
K [auth J]PF00281Ribosomal protein L5 (Ribosomal_L5)Ribosomal protein L5Domain
K [auth J]PF01907Ribosomal protein L37e (Ribosomal_L37e)Ribosomal protein L37e- Family
K [auth J]PF00673ribosomal L5P family C-terminus (Ribosomal_L5_C)ribosomal L5P family C-terminusThis region is found associated with Pfam:PF00281. Domain
PF00832Ribosomal L39 protein (Ribosomal_L39)Ribosomal L39 protein- Family
PF01294Ribosomal protein L13e (Ribosomal_L13e)Ribosomal protein L13e- Family
PF08153NGP1NT (NUC091) domain (NGP1NT)NGP1NT (NUC091) domainThis N terminal domain is found in a subfamily of hypothetical nucleolar GTP-binding proteins similar to human NGP1 [1]. Domain
PF01929Ribosomal protein L14 (Ribosomal_L14e)Ribosomal protein L14- Family
PF00467KOW motif (KOW)KOW motif- Family
PF00827Ribosomal L15 (Ribosomal_L15e)Ribosomal L15- Family
PF06732Pescadillo N-terminus (Pescadillo_N)Pescadillo N-terminus- Family
PF00572Ribosomal protein L13 (Ribosomal_L13)Ribosomal protein L13- Family
PF00237Ribosomal protein L22p/L17e (Ribosomal_L22)Ribosomal protein L22p/L17eThis family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. Domain
PF01780Ribosomal L37ae protein family (Ribosomal_L37ae)Ribosomal L37ae protein family- Family
PF01280Ribosomal protein L19e, N-terminal domain (Ribosomal_L19e)Ribosomal protein L19e, N-terminal domainThis domain is found at the N-terminal end of the large ribosomal subunit protein eL19 found in eukaryotes and archaea. This is an helical domain that assumes an orthogonal bundle topology. Domain
PF25476Ribosomal protein L19e, C-terminal domain (Ribosomal_L19e_C)Ribosomal protein L19e, C-terminal domainThis domain is found at the C-terminal end of the large ribosomal subunit protein eL19 found in eukaryotes and archaea. This is an helical domain that assumes an orthogonal bundle topology. Domain
PF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
PF08701GNL3L/Grn1 putative GTPase (GN3L_Grn1)GNL3L/Grn1 putative GTPase- Family
PF01775Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A (Ribosomal_L18A)Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18AThis family includes: archaeal 50S ribosomal protein L18Ae, often referred to as L20e or LX; fungal 60S ribosomal protein L20; and higher eukaryote 60S ribosomal protein L18A. Domain
PF01246Ribosomal protein L24e (Ribosomal_L24e)Ribosomal protein L24eDomain
PF01776Ribosomal L22e protein family (Ribosomal_L22e)Ribosomal L22e protein family- Family
PF00238Ribosomal protein L14p/L23e (Ribosomal_L14)Ribosomal protein L14p/L23eDomain
PF04427Brix domain (Brix)Brix domainDomain
PF08154NLE (NUC135) domain (NLE)NLE (NUC135) domainThis domain is located N terminal to WD40 repeats. It is found in the microtubule-associated protein Swiss:Q12024 [1]. Domain
PF00276Ribosomal protein L23 (Ribosomal_L23)Ribosomal protein L23- Family
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF01912eIF-6 family (eIF-6)eIF-6 family- Family
PF16906Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26)Ribosomal proteins L26 eukaryotic, L24P archaeal- Family
PF00467KOW motif (KOW)KOW motif- Family
PF01777Ribosomal L27e protein family (Ribosomal_L27e)Ribosomal L27e protein family- Family
BB [auth KK]PF08066PMC2NT (NUC016) domain (PMC2NT)PMC2NT (NUC016) domainThis domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components [1]. Domain
CB [auth LL]PF04000Sas10/Utp3/C1D family (Sas10_Utp3)Sas10/Utp3/C1D family- Family
DB [auth MM]PF08148DSHCT (NUC185) domain (DSHCT)DSHCT (NUC185) domainThis C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [1]. Domain
DB [auth MM]PF00270DEAD/DEAH box helicase (DEAD)DEAD/DEAH box helicaseMembers of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Domain
DB [auth MM]PF00271Helicase conserved C-terminal domain (Helicase_C)Helicase conserved C-terminal domainThe Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Domain
DB [auth MM]PF21408Exosome RNA helicase MTR4-like, stalk (MTR4-like_stalk)Exosome RNA helicase MTR4-like, stalkExosome RNA helicase MTR4 is a conserved RNA helicase that functions together with the nuclear exosome and it is involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclear RNA surveillance pathways involv ...Exosome RNA helicase MTR4 is a conserved RNA helicase that functions together with the nuclear exosome and it is involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclear RNA surveillance pathways involving the so-called TRAMP complex [1,2]. It contains an arch domain, required for proper 5.8S rRNA processing, and appears to function independently of canonical helicase activity [3]. The arch domain comprises an helical stalk/elbow that flanks a KOW module which adopts a beta-barrel fold. This entry represents the helical stalk found at the N-terminal of KOW beta-barrel from MTR4 [1-3]. This entry also includes Ski2-like helicases which have an overall similar structure to MTR4 proteins. However, Ski2 from yeast does not have the KOW motif and the beta-barrel is tightly packed against the helical stalk [3].
Domain
DB [auth MM]PF13234Mtr4-like, beta-barrel domain (MTR4_beta-barrel)Mtr4-like, beta-barrel domainExosome RNA helicase Mtr4 is a essential RNA helicase, and is an exosome-activating cofactor. It functions together with the nuclear exosome being involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclea ...Exosome RNA helicase Mtr4 is a essential RNA helicase, and is an exosome-activating cofactor. It functions together with the nuclear exosome being involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclear RNA surveillance pathways involving the so-called TRAMP complex [1,2,3]. It contains an arch domain, required for proper 5.8S rRNA processing, and appears to function independently of canonical helicase activity [3]. The arch domain comprises an helical stalk/elbow that flanks a KOW module which adopts a beta-barrel fold. This entry represents the beta-barrel of MTR4 and related Ski2-like helicases. Ski2 from yeast has an overall similar structure to MTR4 proteins. However, it does not have the KOW motif [4] and it is not included in this entry.
Domain
PF04939Ribosome biogenesis regulatory protein (RRS1) (RRS1)Ribosome biogenesis regulatory protein (RRS1)- Family
PF17777Insertion domain in 60S ribosomal protein L10P (RL10P_insert)Insertion domain in 60S ribosomal protein L10PThis domain is found in prokaryotic and archaeal ribosomal L10 protein [1]. Domain
PF00466Ribosomal protein L10 (Ribosomal_L10)Ribosomal protein L10- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth 2]7S ribosomal RNA---
B [auth A]60S ribosomal protein L2-A
C [auth B]60S ribosomal protein L3
D [auth C]60S ribosomal protein L4-A
E [auth D]60S ribosomal protein L5
F [auth E]60S ribosomal protein L6-A
G [auth F]60S ribosomal protein L7-A
H [auth G]60S ribosomal protein L8-A
I [auth H]60S ribosomal protein L9-A
J [auth I]Bud site selection protein 20
K [auth J]60S ribosomal protein L11-A
60S ribosomal protein L13-A
60S ribosomal protein L14-A
60S ribosomal protein L15-A
60S ribosomal protein L16-A
60S ribosomal protein L17-A
60S ribosomal protein L18-A
60S ribosomal protein L19-A
60S ribosomal protein L20-A
60S ribosomal protein L21-A
60S ribosomal protein L22-A
60S ribosomal protein L23-A
60S ribosomal protein L25
60S ribosomal protein L26-A
60S ribosomal protein L27-A
AA [auth a]60S ribosomal protein L28
BA [auth b]Nucleolar GTP-binding protein 1
DA [auth d]60S ribosomal protein L31-A
EA [auth e]60S ribosomal protein L32
FA [auth f]60S ribosomal protein L33-A
GA [auth g]60S ribosomal protein L34-A
HA [auth h]60S ribosomal protein L35-A
IA [auth i]60S ribosomal protein L36-A
JA [auth j]60S ribosomal protein L37-A
KA [auth k]60S ribosomal protein L38
LA [auth l]60S ribosomal protein L39
MA [auth m]Nucleolar GTP-binding protein 2
NA [auth n]Pescadillo homolog
OA [auth p]60S ribosomal protein L43-A
PA [auth r]Ribosome biogenesis protein NSA2-
QA [auth s]Nuclear GTP-binding protein NUG1
RA [auth u]Ribosome biogenesis protein RLP24
SA [auth v]Ribosome biogenesis protein RPF2
TA [auth w]Regulator of ribosome biosynthesis-
UA [auth x]Ribosome assembly protein 4-
VA [auth y]Eukaryotic translation initiation factor 6
WA [auth z]UPF0642 protein YBL028C- -
XA [auth 1]25S ribosomal RNA---
YA [auth 3]5S ribosomal RNA---
ZA [auth 4]Probable metalloprotease ARX1
AB [auth 5]rRNA-processing protein CGR1-
BB [auth KK]Exosome complex exonuclease RRP6
CB [auth LL]Exosome complex protein LRP1
DB [auth MM]ATP-dependent RNA helicase DOB1
EB [auth NN]MPP6---
CA [auth c]60S ribosomal protein L30
Ribosome assembly factor MRT4

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
B [auth A]IPR022669Large ribosomal subunit protein uL2, C-terminalDomain
B [auth A]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
B [auth A]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
B [auth A]IPR022671Large ribosomal subunit protein uL2, conserved siteConserved Site
B [auth A]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
B [auth A]IPR022666Large ribosomal subunit protein uL2, RNA-binding domainDomain
B [auth A]IPR014726Large ribosomal subunit protein uL2, domain 3Homologous Superfamily
B [auth A]IPR002171Large ribosomal subunit protein uL2Family
C [auth B]IPR019926Large ribosomal subunit protein uL3, conserved siteConserved Site
C [auth B]IPR044892Ribosomal protein L3, domain 3, archaeal-type superfamilyHomologous Superfamily
C [auth B]IPR000597Large ribosomal subunit protein uL3Family
C [auth B]IPR045077Large ribosomal subunit protein uL3, archaea/eukaryotaFamily
C [auth B]IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
D [auth C]IPR025755Large ribosomal subunit protein uL4, C-terminal domainDomain
D [auth C]IPR002136Large ribosomal subunit protein uL4Family
D [auth C]IPR013000Large ribosomal subunit protein uL4, eukaryota/archaea, conserved siteConserved Site
D [auth C]IPR045240Large ribosomal subunit protein uL4, eukaryota/archaeaFamily
D [auth C]IPR023574Large ribosomal subunit protein uL4 domain superfamilyHomologous Superfamily
E [auth D]IPR057268Large ribosomal subunit protein uL18Family
E [auth D]IPR005485Large ribosomal subunit protein uL18, eukaryota/archaeaFamily
E [auth D]IPR025607Large ribosomal subunit protein uL18, C-terminal, eukaryotesDomain
F [auth E]IPR049633Large ribosomal subunit protein eL6, conserved siteConserved Site
F [auth E]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
F [auth E]IPR041997Large ribosomal subunit protein eL6, KOW domainDomain
F [auth E]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
F [auth E]IPR000915Large ribosomal subunit protein eL6Family
G [auth F]IPR036919Large ribosomal subunit protein uL30, ferredoxin-like fold domain superfamilyHomologous Superfamily
G [auth F]IPR035808Large ribosomal subunit protein uL30, eukaryota/archaeaDomain
G [auth F]IPR005998Large ribosomal subunit protein uL30, eukaryotaFamily
G [auth F]IPR039699Large ribosomal subunit protein uL30Family
G [auth F]IPR012988Large ribosomal subunit protein uL30, N-terminal, eukaryotaDomain
G [auth F]IPR016082Large ribosomal subunit protein uL30-like, ferredoxin-like fold domainDomain
G [auth F]IPR018038Large ribosomal subunit protein uL30, conserved siteConserved Site
H [auth G]IPR050257Large ribosomal subunit protein eL8/uL1-likeFamily
H [auth G]IPR004038Ribosomal protein eL8/eL30/eS12/Gadd45Domain
H [auth G]IPR004037Large ribosomal subunit protein eL8-like, conserved siteConserved Site
H [auth G]IPR029064Ribosomal protein eL30-like superfamilyHomologous Superfamily
H [auth G]IPR018492Ribosomal protein eL8/Nhp2 familyFamily
H [auth G]IPR001921Large ribosomal subunit protein eL8, eukaryotaFamily
I [auth H]IPR020040Large ribosomal subunit protein uL6, alpha-beta domainDomain
I [auth H]IPR002359Large ribosomal subunit protein uL6, conserved site-2Conserved Site
I [auth H]IPR036789Large ribosomal subunit protein uL6-like, alpha-beta domain superfamilyHomologous Superfamily
I [auth H]IPR000702Large ribosomal subunit protein uL6-likeFamily
J [auth I]IPR003604Matrin/U1-C-like, C2H2-type zinc fingerDomain
J [auth I]IPR051879C2H2-type Zinc Finger Maturation ProteinFamily
J [auth I]IPR013087Zinc finger C2H2-typeDomain
J [auth I]IPR036236Zinc finger C2H2 superfamilyHomologous Superfamily
J [auth I]IPR022755Zinc finger, double-stranded RNA bindingDomain
K [auth J]IPR020929Large ribosomal subunit protein uL5, conserved siteConserved Site
K [auth J]IPR022803Large ribosomal subunit protein uL5 domain superfamilyHomologous Superfamily
K [auth J]IPR031309Large ribosomal subunit protein uL5, C-terminalDomain
K [auth J]IPR057266Large ribosomal subunit protein uL5, eukaryota/archaeaFamily
K [auth J]IPR031310Large ribosomal subunit protein uL5, N-terminalDomain
K [auth J]IPR002132Large ribosomal subunit protein uL5Family
IPR001380Large ribosomal subunit protein eL13Family
IPR018256Large ribosomal subunit protein eL13, conserved siteConserved Site
IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
IPR039660Large ribosomal subunit protein eL14Family
IPR002784Large ribosomal subunit protein eL14 domainDomain
IPR005824KOWDomain
IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
IPR020925Large ribosomal subunit protein eL15, conserved siteConserved Site
IPR024794Large ribosomal subunit protein eL15 core domain superfamilyHomologous Superfamily
IPR000439Large ribosomal subunit protein eL15Family
IPR023563Large ribosomal subunit protein uL13, conserved siteConserved Site
IPR005822Large ribosomal subunit protein uL13Family
IPR036899Large ribosomal subunit protein uL13 superfamilyHomologous Superfamily
IPR005755Large ribosomal subunit protein uL13, eukaryota/archaeaFamily
IPR018260Large ribosomal subunit protein uL22, conserved siteConserved Site
IPR005721Large ribosomal subunit protein uL22, eukaryota/archaeaFamily
IPR036394Ribosomal protein uL22 superfamilyHomologous Superfamily
IPR001063Large ribosomal subunit protein uL22Family
IPR021131Large ribosomal subunit protein uL15/eL18Domain
IPR021132Large ribosomal subunit protein eL18, conserved siteConserved Site
IPR000039Large ribosomal subunit protein eL18Family
IPR036227Large ribosomal subunit protein uL15/eL18 superfamilyHomologous Superfamily
IPR039547Large ribosomal subunit protein eL19Family
IPR023638Large ribosomal subunit protein eL19, conserved siteConserved Site
IPR057260Ribosomal protein L19e, C-terminal domainDomain
IPR033935Large ribosomal subunit protein eL19, eukaryoticDomain
IPR015972Large ribosomal subunit protein eL19, domain 1Homologous Superfamily
IPR057259Ribosomal protein L19e, N-terminal domainDomain
IPR035970Large ribosomal subunit protein eL19 superfamilyHomologous Superfamily
IPR000196Large ribosomal subunit protein eL19 domainDomain
IPR028877Large ribosomal subunit protein eL20Family
IPR023573Large ribosomal subunit protein eL20 domainDomain
IPR021138Large ribosomal subunit protein eL20, eukaryotaFamily
IPR018259Large ribosomal subunit protein eL21, conserved siteConserved Site
IPR036948Large ribosomal subunit protein eL21 superfamilyHomologous Superfamily
IPR001147Large ribosomal subunit protein eL21Family
IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
IPR002671Large ribosomal subunit protein eL22Family
IPR038526Large ribosomal subunit protein eL22 superfamilyHomologous Superfamily
IPR036853Large ribosomal subunit protein uL14 superfamilyHomologous Superfamily
IPR000218Large ribosomal subunit protein uL14Family
IPR019972Large ribosomal subunit protein uL14, conserved siteConserved Site
IPR001014Large ribosomal subunit protein uL23, conserved siteConserved Site
IPR013025Large ribosomal subunit protein uL23-likeFamily
IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
IPR005633Large ribosomal subunit protein uL23, N-terminalDomain
IPR005756Large ribosomal subunit protein uL24, eukaryota_archaeaFamily
IPR041988Large ribosomal subunit protein uL24, KOW domainDomain
IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
IPR005824KOWDomain
IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
IPR005825Large ribosomal subunit protein uL24, conserved siteConserved Site
IPR018262Large ribosomal subunit protein eL27, conserved siteConserved Site
IPR038655Large ribosomal subunit protein eL27 superfamilyHomologous Superfamily
IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
IPR001141Large ribosomal subunit protein eL27Family
IPR041991Large ribosomal subunit protein eL27, KOW domainDomain
AA [auth a]IPR021131Large ribosomal subunit protein uL15/eL18Domain
AA [auth a]IPR030878Large ribosomal subunit protein uL15Family
AA [auth a]IPR001196Large ribosomal subunit protein uL15, conserved siteConserved Site
AA [auth a]IPR036227Large ribosomal subunit protein uL15/eL18 superfamilyHomologous Superfamily
BA [auth b]IPR024926Nucleolar GTP-binding protein 1Family
BA [auth b]IPR031167OBG-type guanine nucleotide-binding (G) domainDomain
BA [auth b]IPR012973NOG, C-terminalDomain
BA [auth b]IPR010674Nucleolar GTP-binding protein 1, Rossman-fold domainDomain
BA [auth b]IPR041623NOG1, N-terminal helical domainDomain
BA [auth b]IPR006073GTP binding domainDomain
BA [auth b]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
DA [auth d]IPR020052Large ribosomal subunit protein eL31, conserved siteConserved Site
DA [auth d]IPR023621Large ribosomal subunit protein eL31 domain superfamilyHomologous Superfamily
DA [auth d]IPR000054Large ribosomal subunit protein eL31Family
EA [auth e]IPR036351Large ribosomal subunit protein eL32 superfamilyHomologous Superfamily
EA [auth e]IPR001515Large ribosomal subunit protein eL32Family
EA [auth e]IPR018263Large ribosomal subunit protein eL32, conserved siteConserved Site
FA [auth f]IPR038661Large ribosomal subunit protein eL33 superfamilyHomologous Superfamily
FA [auth f]IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
FA [auth f]IPR001780Large ribosomal subunit protein eL33Family
FA [auth f]IPR018266Large ribosomal subunit protein eL33, conserved siteConserved Site
GA [auth g]IPR008195Large ribosomal subunit protein eL34Family
GA [auth g]IPR038562Large ribosomal subunit protein eL34, C-terminal domain superfamilyHomologous Superfamily
GA [auth g]IPR018065Large ribosomal subunit protein eL34, conserved siteConserved Site
HA [auth h]IPR001854Large ribosomal subunit protein uL29Family
HA [auth h]IPR036049Large ribosomal subunit protein uL29 superfamilyHomologous Superfamily
HA [auth h]IPR018254Large ribosomal subunit protein uL29, conserved siteConserved Site
HA [auth h]IPR045059Large ribosomal subunit protein uL29, eukaryotaFamily
IA [auth i]IPR000509Large ribosomal subunit protein eL36Family
IA [auth i]IPR038097Large ribosomal subunit protein eL36 domain superfamilyHomologous Superfamily
JA [auth j]IPR011331Large ribosomal subunit protein eL37/eL43Homologous Superfamily
JA [auth j]IPR001569Large ribosomal subunit protein eL37Family
JA [auth j]IPR018267Large ribosomal subunit protein eL37, conserved siteConserved Site
JA [auth j]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
KA [auth k]IPR002675Large ribosomal subunit protein eL38Family
KA [auth k]IPR038464Large ribosomal subunit protein eL38 superfamilyHomologous Superfamily
LA [auth l]IPR023626Large ribosomal subunit protein eL39 domain superfamilyHomologous Superfamily
LA [auth l]IPR000077Large ribosomal subunit protein eL39Family
LA [auth l]IPR020083Large ribosomal subunit protein eL39, conserved siteConserved Site
MA [auth m]IPR050755TRAFAC YlqF/YawG GTPases, Ribosome MaturationFamily
MA [auth m]IPR030378Circularly permuted (CP)-type guanine nucleotide-binding (G) domainDomain
MA [auth m]IPR024929Nucleolar GTP-binding protein 2, circularly permuted GTPase motifDomain
MA [auth m]IPR006073GTP binding domainDomain
MA [auth m]IPR012971Nucleolar GTP-binding protein 2, N-terminal domainDomain
MA [auth m]IPR023179GTP-binding protein, orthogonal bundle domain superfamilyHomologous Superfamily
MA [auth m]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
NA [auth n]IPR010613PescadilloFamily
NA [auth n]IPR001357BRCT domainDomain
NA [auth n]IPR036420BRCT domain superfamilyHomologous Superfamily
OA [auth p]IPR002674Large ribosomal subunit protein eL43Family
OA [auth p]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
OA [auth p]IPR011331Large ribosomal subunit protein eL37/eL43Homologous Superfamily
OA [auth p]IPR050522Eukaryotic ribosomal protein eL43Family
PA [auth r]IPR039411Ribosomal biogenesis NSA2 familyFamily
PA [auth r]IPR022309Ribosomal protein eS8/ribosomal biogenesis NSA2Family
QA [auth s]IPR050755TRAFAC YlqF/YawG GTPases, Ribosome MaturationFamily
QA [auth s]IPR030378Circularly permuted (CP)-type guanine nucleotide-binding (G) domainDomain
QA [auth s]IPR006073GTP binding domainDomain
QA [auth s]IPR014813Guanine nucleotide-binding protein-like 3, N-terminal domainDomain
QA [auth s]IPR023179GTP-binding protein, orthogonal bundle domain superfamilyHomologous Superfamily
QA [auth s]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
RA [auth u]IPR011017TRASH domainDomain
RA [auth u]IPR000988Large ribosomal subunit protein eL24-related, N-terminalDomain
RA [auth u]IPR038630Ribosomal protein L24e/L24 superfamilyHomologous Superfamily
RA [auth u]IPR056366Large ribosomal subunit protein eL24Family
SA [auth v]IPR039770Ribosome biogenesis protein Rpf2Family
SA [auth v]IPR007109Brix domainDomain
TA [auth w]IPR007023Ribosomal biogenesis regulatory proteinFamily
UA [auth x]IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
UA [auth x]IPR001680WD40 repeatRepeat
UA [auth x]IPR019775WD40 repeat, conserved siteConserved Site
UA [auth x]IPR012972NLEDomain
UA [auth x]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
UA [auth x]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
VA [auth y]IPR002769Translation initiation factor IF6Family
WA [auth z]IPR019434Domain of unknown function DUF2423Domain
ZA [auth 4]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
ZA [auth 4]IPR047113Proliferation-associated protein 2G4/ARX1Family
ZA [auth 4]IPR036005Creatinase/aminopeptidase-likeHomologous Superfamily
AB [auth 5]IPR005579Cgr1-likeFamily
BB [auth KK]IPR036397Ribonuclease H superfamilyHomologous Superfamily
BB [auth KK]IPR002121HRDC domainDomain
BB [auth KK]IPR012588Exosome-associated factor Rrp6, N-terminalDomain
BB [auth KK]IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
BB [auth KK]IPR045092Exosome complex exonuclease Rrp6-likeFamily
BB [auth KK]IPR0025623'-5' exonuclease domainDomain
BB [auth KK]IPR049559Rrp6-like, 3'-5' exonuclease domainDomain
BB [auth KK]IPR010997HRDC-like superfamilyHomologous Superfamily
BB [auth KK]IPR044876HRDC domain superfamilyHomologous Superfamily
CB [auth LL]IPR011082Exosome-associated factor Rrp47/DNA strand repair C1DFamily
CB [auth LL]IPR007146Sas10/Utp3/C1DFamily
DB [auth MM]IPR048392Exosome RNA helicase MTR4-like, stalkDomain
DB [auth MM]IPR012961ATP-dependent RNA helicase Ski2/MTR4, C-terminalDomain
DB [auth MM]IPR025696Exosome RNA helicase MTR4-like, beta-barrel domainDomain
DB [auth MM]IPR016438Circadian oscillator component FRH-likeFamily
DB [auth MM]IPR011545DEAD/DEAH-box helicase domainDomain
DB [auth MM]IPR011254Prismane-like superfamilyHomologous Superfamily
DB [auth MM]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
DB [auth MM]IPR001650Helicase, C-terminal domain-likeDomain
DB [auth MM]IPR050699ATP-dependent RNA helicase SUPV3-likeFamily
DB [auth MM]IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
CA [auth c]IPR022991Large ribosomal subunit protein eL30, conserved siteConserved Site
CA [auth c]IPR004038Ribosomal protein eL8/eL30/eS12/Gadd45Domain
CA [auth c]IPR039109Large ribosomal subunit protein eL30-likeFamily
CA [auth c]IPR029064Ribosomal protein eL30-like superfamilyHomologous Superfamily
IPR043141Large ribosomal subunit protein uL10-like domain superfamilyHomologous Superfamily
IPR043164Large ribosomal subunit protein uL10-like, insertion domain superfamilyHomologous Superfamily
IPR001790Large ribosomal subunit protein uL10, N-terminalDomain
IPR051742Ribosomal Assembly Factor uL10Family
IPR040637Large ribosomal subunit protein uL10-like, insertion domainDomain
IPR033867Ribosome assembly factor Mrt4Family