8I9T | pdb_00008i9t

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-1

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
TA [auth Lf]SCOP2B SuperfamilyTranslational proteins 8106190 3000811 SCOP2B (2022-06-29)
SA [auth Le]SCOP2B SuperfamilyRibosomal protein L32e 8106182 3000982 SCOP2B (2022-06-29)
RA [auth LY]SCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain 8106166 3000334 SCOP2B (2022-06-29)
PA [auth LV]SCOP2B Superfamily50S Ribosomal protein L14-like 8106208 3000433 SCOP2B (2022-06-29)
JA [auth LN]SCOP2B SuperfamilyRibosomal proteins S24e, L23 and L15e 8106168 3000210 SCOP2B (2022-06-29)
BA [auth LC]SCOP2B SuperfamilyRibosomal protein L4 8077111 3001146 SCOP2B (2022-06-29)
AA [auth LB]SCOP2B SuperfamilyTranslational proteins 8106162 3000811 SCOP2B (2022-06-29)
P [auth CN]SCOP2B SuperfamilyPentein 8084662 3000640 SCOP2B (2022-06-29)
M [auth CK]SCOP2B Superfamily50S Ribosomal protein L14-like 8053081 3000433 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
I [auth CG]F_UNCLASSIFIEDe8i9tCG1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: PUA domainF: F_UNCLASSIFIEDECOD (1.6)
I [auth CG]F_UNCLASSIFIEDe8i9tCG2 A: a+b two layersX: Cystatin-likeH: Pre-PUA domain (From Topology)T: Pre-PUA domainF: F_UNCLASSIFIEDECOD (1.6)
H [auth CF]F_UNCLASSIFIEDe8i9tCF1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein L10-like (From Topology)T: Ribosomal protein L10-likeF: F_UNCLASSIFIEDECOD (1.6)
H [auth CF]F_UNCLASSIFIEDe8i9tCF2 A: a+b two layersX: Insertion domain in 60S ribosomal protein rpP0 (L10P) (From Topology)H: Insertion domain in 60S ribosomal protein rpP0 (L10P) (From Topology)T: Insertion domain in 60S ribosomal protein rpP0 (L10P)F: F_UNCLASSIFIEDECOD (1.6)
CB [auth Cg]F_UNCLASSIFIEDe8i9tCg1 A: a/b three-layered sandwichesX: Anticodon-binding domain of Class II aaRS (From Topology)H: Anticodon-binding domain of Class II aaRS (From Topology)T: Anticodon-binding domain of Class II aaRSF: F_UNCLASSIFIEDECOD (1.6)
YA [auth Cc]F_UNCLASSIFIEDe8i9tCc1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: F_UNCLASSIFIEDECOD (1.6)
XA [auth Lq]F_UNCLASSIFIEDe8i9tLq2 A: a+b two layersX: a+b domain in Ribosomal protein L1 (From Topology)H: a+b domain in Ribosomal protein L1 (From Topology)T: a+b domain in Ribosomal protein L1F: F_UNCLASSIFIEDECOD (1.6)
XA [auth Lq]F_UNCLASSIFIEDe8i9tLq1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Rossmann-like domain in Ribosomal protein L1 (From Topology)T: Rossmann-like domain in Ribosomal protein L1F: F_UNCLASSIFIEDECOD (1.6)
WA [auth Lj]F_UNCLASSIFIEDe8i9tLj1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: F_UNCLASSIFIEDECOD (1.6)
VA [auth Li]F_UNCLASSIFIEDe8i9tLi1 A: alpha arraysX: 60S ribosomal protein rpL36 (L36e) (From Topology)H: 60S ribosomal protein rpL36 (L36e) (From Topology)T: 60S ribosomal protein rpL36 (L36e)F: F_UNCLASSIFIEDECOD (1.6)
UA [auth Lh]F_UNCLASSIFIEDe8i9tLh1 A: alpha bundlesX: Long alpha-hairpinH: Ribosomal protein L29 (L29p) (From Topology)T: Ribosomal protein L29 (L29p)F: F_UNCLASSIFIEDECOD (1.6)
TA [auth Lf]F_UNCLASSIFIEDe8i9tLf1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: F_UNCLASSIFIEDECOD (1.6)
SA [auth Le]F_UNCLASSIFIEDe8i9tLe1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal protein L32e (From Topology)T: Ribosomal protein L32eF: F_UNCLASSIFIEDECOD (1.6)
RA [auth LY]F_UNCLASSIFIEDe8i9tLY1 A: beta barrelsX: SH3H: SH3T: SH3F: F_UNCLASSIFIEDECOD (1.6)
PA [auth LV]F_UNCLASSIFIEDe8i9tLV1 A: beta barrelsX: Ribosomal protein L14-likeH: Ribosomal protein L14-related (From Topology)T: Ribosomal protein L14-relatedF: F_UNCLASSIFIEDECOD (1.6)
OA [auth LT]F_UNCLASSIFIEDe8i9tLT1 A: beta barrelsX: SH3H: SH3T: SH3F: F_UNCLASSIFIEDECOD (1.6)
NA [auth LS]F_UNCLASSIFIEDe8i9tLS1 A: a+b two layersX: GP2-likeH: RplX-like (From Topology)T: RplX-likeF: F_UNCLASSIFIEDECOD (1.6)
MA [auth LQ]F_UNCLASSIFIEDe8i9tLQ1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal proteins L15p and L18e (From Topology)T: Ribosomal proteins L15p and L18eF: F_UNCLASSIFIEDECOD (1.6)
LA [auth LP]F_UNCLASSIFIEDe8i9tLP1 A: a+b two layersX: Enolase-N/ribosomal proteinH: Ribosomal protein L22 (From Topology)T: Ribosomal protein L22F: F_UNCLASSIFIEDECOD (1.6)
KA [auth LO]F_UNCLASSIFIEDe8i9tLO1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal protein L13 and L16-A (From Topology)T: Ribosomal protein L13 and L16-AF: F_UNCLASSIFIEDECOD (1.6)
JA [auth LN]F_UNCLASSIFIEDe8i9tLN1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal proteins S24e, L23 and L15e (From Topology)T: Ribosomal proteins S24e, L23 and L15eF: F_UNCLASSIFIEDECOD (1.6)
IA [auth LM]F_UNCLASSIFIEDe8i9tLM1 A: beta barrelsX: SH3H: SH3T: SH3F: F_UNCLASSIFIEDECOD (1.6)
HA [auth LL]F_UNCLASSIFIEDe8i9tLL1 A: extended segmentsX: RPL13 (From Topology)H: RPL13 (From Topology)T: RPL13F: F_UNCLASSIFIEDECOD (1.6)
GA [auth LK]F_UNCLASSIFIEDe8i9tLK2 A: alpha arraysX: HTHH: HTHT: Ribosomal protein L11, C-terminal domainF: F_UNCLASSIFIEDECOD (1.6)
GA [auth LK]F_UNCLASSIFIEDe8i9tLK1 A: a+b two layersX: Ribosomal protein L11/L12e N-terminal domain-likeH: Ribosomal protein L11/L12e N-terminal domain (From Topology)T: Ribosomal protein L11/L12e N-terminal domainF: F_UNCLASSIFIEDECOD (1.6)
FA [auth LH]F_UNCLASSIFIEDe8i9tLH2 A: a+b two layersX: Ribosomal protein L6 (From Topology)H: Ribosomal protein L6 (From Topology)T: Ribosomal protein L6F: F_UNCLASSIFIEDECOD (1.6)
EA [auth LG]F_UNCLASSIFIEDe8i9tLG1 A: a+b three layersX: Bacillus chorismate mutase-likeH: L30e-like (From Topology)T: L30e-likeF: F_UNCLASSIFIEDECOD (1.6)
CA [auth LE]F_UNCLASSIFIEDe8i9tLE1 A: beta barrelsX: SH3H: SH3T: SH3F: F_UNCLASSIFIEDECOD (1.6)
BA [auth LC]F_UNCLASSIFIEDe8i9tLC1 A: a/b three-layered sandwichesX: Ribosomal protein L4 (From Topology)H: Ribosomal protein L4 (From Topology)T: Ribosomal protein L4F: F_UNCLASSIFIEDECOD (1.6)
BA [auth LC]F_UNCLASSIFIEDe8i9tLC2 A: extended segmentsX: C-terminal helical region in 60S ribosomal protein L4 (L4p) (From Topology)H: C-terminal helical region in 60S ribosomal protein L4 (L4p) (From Topology)T: C-terminal helical region in 60S ribosomal protein L4 (L4p)F: F_UNCLASSIFIEDECOD (1.6)
AA [auth LB]F_UNCLASSIFIEDe8i9tLB1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: F_UNCLASSIFIEDECOD (1.6)
R [auth CP]F_UNCLASSIFIEDe8i9tCP2 A: a+b two layersX: Alpha-beta plaitsH: NOL1/NOP2/sun N-terminal ferredoxin-like domain (From Topology)T: NOL1/NOP2/sun N-terminal ferredoxin-like domainF: F_UNCLASSIFIEDECOD (1.6)
R [auth CP]F_UNCLASSIFIEDe8i9tCP1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: S-adenosyl-L-methionine-dependent methyltransferasesF: F_UNCLASSIFIEDECOD (1.6)
P [auth CN]F_UNCLASSIFIEDe8i9tCN1 A: a+b duplicates or obligate multimersX: Pentein (From Topology)H: Pentein (From Topology)T: PenteinF: F_UNCLASSIFIEDECOD (1.6)
O [auth CM]F_UNCLASSIFIEDe8i9tCM1 A: a+b two layersX: Ribosomal protein L30p/L7e (From Topology)H: Ribosomal protein L30p/L7e (From Topology)T: Ribosomal protein L30p/L7eF: F_UNCLASSIFIEDECOD (1.6)
DA [auth LF]F_UNCLASSIFIEDe8i9tLF1 A: a+b two layersX: Ribosomal protein L30p/L7e (From Topology)H: Ribosomal protein L30p/L7e (From Topology)T: Ribosomal protein L30p/L7eF: F_UNCLASSIFIEDECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I [auth CG]PF03657UPF0113 PUA domain (UPF0113)UPF0113 PUA domainDomain
I [auth CG]PF04427Brix domain (Brix)Brix domainDomain
I [auth CG]PF17833NIP7/UPF0113, pre-PUA domain (pre-PUA_NIP7)NIP7/UPF0113, pre-PUA domainThis entry represents the N-terminal, pre-PUA domain of yeast 60S ribosome subunit biogenesis protein NIP7 and homologues, some uncharacterised proteins from the UPF0113 family and similar sequences from eukaryotes and some archaeal species. NIP7 is ...This entry represents the N-terminal, pre-PUA domain of yeast 60S ribosome subunit biogenesis protein NIP7 and homologues, some uncharacterised proteins from the UPF0113 family and similar sequences from eukaryotes and some archaeal species. NIP7 is required for proper 27S pre-rRNA processing and 60S ribosome subunit assembly. This domain is found associated with Pfam:PF03657.
Domain
H [auth CF]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
H [auth CF]PF00466Ribosomal protein L10 (Ribosomal_L10)Ribosomal protein L10- Family
G [auth CE]PF01778Ribosomal L28e protein family (Ribosomal_L28e)Ribosomal L28e protein family- Family
G [auth CE]PF13959ATP-dependent rRNA helicase SPB4-like, C-terminal extension (CTE_SPB4)ATP-dependent rRNA helicase SPB4-like, C-terminal extensionThis short domain is found at the C-terminus of many helicase proteins, including ATP-dependent rRNA helicase SPB4 from Saccharomyces cerevisiae, which is involved in the biogenesis of 60S ribosomal subunits. SPB4 is organised into four domains: dual ...This short domain is found at the C-terminus of many helicase proteins, including ATP-dependent rRNA helicase SPB4 from Saccharomyces cerevisiae, which is involved in the biogenesis of 60S ribosomal subunits. SPB4 is organised into four domains: dual RecA domains (Pfam:PF00270 and Pfam:PF00271), a C-terminal extension (CTE, represented by this entry) and a C-terminal tail (Pfam:PF23681). This domain packs closely onto the catalytic core and engages the four nucleotides immediately 5' to those within the RNA binding pocket. It shows a mainly alpha- helical structure [1].
Domain
G [auth CE]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
G [auth CE]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
G [auth CE]PF04874Mak16 protein C-terminal region (Mak16)Mak16 protein C-terminal region- Family
F [auth CC]PF08145BOP1NT (NUC169) domain (BOP1NT)BOP1NT (NUC169) domainThis N terminal domain is found in BOP1-like WD40 proteins [1]. Domain
F [auth CC]PF05997Nucleolar protein,Nop52 (Nop52)Nucleolar protein,Nop52- Family
E [auth CB]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
E [auth CB]PF00687Ribosomal protein L1p/L10e family (Ribosomal_L1)Ribosomal protein L1p/L10e familyThis family includes prokaryotic L1 and eukaryotic L10. Domain
RA [auth LY]PF16906Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26)Ribosomal proteins L26 eukaryotic, L24P archaeal- Family
RA [auth LY]PF00467KOW motif (KOW)KOW motif- Family
QA [auth LX]PF03939Ribosomal protein L23, N-terminal domain (Ribosomal_L23eN)Ribosomal protein L23, N-terminal domain- Family
PA [auth LV]PF00238Ribosomal protein L14p/L23e (Ribosomal_L14)Ribosomal protein L14p/L23eDomain
D [auth CA]PF04427Brix domain (Brix)Brix domainDomain
NA [auth LS]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
MA [auth LQ]PF00687Ribosomal protein L1p/L10e family (Ribosomal_L1)Ribosomal protein L1p/L10e familyThis family includes prokaryotic L1 and eukaryotic L10. Domain
LA [auth LP]PF00237Ribosomal protein L22p/L17e (Ribosomal_L22)Ribosomal protein L22p/L17eThis family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. Domain
KA [auth LO]PF00572Ribosomal protein L13 (Ribosomal_L13)Ribosomal protein L13- Family
JA [auth LN]PF00827Ribosomal L15 (Ribosomal_L15e)Ribosomal L15- Family
IA [auth LM]PF01929Ribosomal protein L14 (Ribosomal_L14e)Ribosomal protein L14- Family
GA [auth LK]PF03946Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N)Ribosomal protein L11, N-terminal domainThe N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain. Domain
GA [auth LK]PF00298Ribosomal protein L11, RNA binding domain (Ribosomal_L11)Ribosomal protein L11, RNA binding domainDomain
FA [auth LH]PF00347Ribosomal protein L6 (Ribosomal_L6)Ribosomal protein L6Domain
FA [auth LH]PF00831Ribosomal L29 protein (Ribosomal_L29)Ribosomal L29 protein- Family
EA [auth LG]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
CA [auth LE]PF01655Ribosomal protein L32 (Ribosomal_L32e)Ribosomal protein L32- Family
CA [auth LE]PF01159Ribosomal protein L6e (Ribosomal_L6e)Ribosomal protein L6e- Family
BA [auth LC]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
BA [auth LC]PF00573Ribosomal protein L4/L1 family (Ribosomal_L4)Ribosomal protein L4/L1 family- Family
V [auth CU]PF05890Eukaryotic rRNA processing protein EBP2 (Ebp2)Eukaryotic rRNA processing protein EBP2- Family
U [auth CS]PF07780Spb1 C-terminal domain (Spb1_C)Spb1 C-terminal domainThis domain is found at the C-terminus of a family of FtsJ-like methyltransferases. Members of this family are involved in 60S ribosomal biogenesis, for example Swiss:P25582 [1]. This domain interacts with the meandering tail of Erb1 and its removal ...This domain is found at the C-terminus of a family of FtsJ-like methyltransferases. Members of this family are involved in 60S ribosomal biogenesis, for example Swiss:P25582 [1]. This domain interacts with the meandering tail of Erb1 and its removal is required to form the pre-mature inter-subunit surface of the Arx1/Nog2 particle [1,2].
Domain
T [auth CR]PF09420Ribosome biogenesis protein Nop16 (Nop16)Ribosome biogenesis protein Nop16- Family
S [auth CQ]PF01246Ribosomal protein L24e (Ribosomal_L24e)Ribosomal protein L24eDomain
R [auth CP]PF0118916S rRNA methyltransferase RsmB/F (Methyltr_RsmB-F)16S rRNA methyltransferase RsmB/FThis is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) posi ...This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA [1,2].
Domain
R [auth CP]PF22458Methyltr_RsmF/B-like, ferredoxin-like domain (RsmF-B_ferredox)Methyltr_RsmF/B-like, ferredoxin-like domainThis entry represents a ferredoxin-like domain found in methyltransferases RsmB, RsmF and related sequences [1-5]. Domain
P [auth CN]PF01912eIF-6 family (eIF-6)eIF-6 family- Family
DA [auth LF],
O [auth CM]		PF08079Ribosomal L30 N-terminal domain (Ribosomal_L30_N)Ribosomal L30 N-terminal domainThis presumed domain is found at the N-terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018 [1]. Domain
DA [auth LF],
O [auth CM]		PF00327Ribosomal protein L30p/L7e (Ribosomal_L30)Ribosomal protein L30p/L7eThis family includes prokaryotic L30 and eukaryotic L7. Domain
DA [auth LF],
O [auth CM]		PF01247Ribosomal protein L35Ae (Ribosomal_L35Ae)Ribosomal protein L35AeThis entry represents the ribosomal eL33 previously known as L35A, eukaryotic and archaebacterial ribosomal proteins. Domain
N [auth CL]PF0192650S ribosome-binding GTPase (MMR_HSR1)50S ribosome-binding GTPase- Family
N [auth CL]PF08701GNL3L/Grn1 putative GTPase (GN3L_Grn1)GNL3L/Grn1 putative GTPase- Family
M [auth CK]PF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
L [auth CJ]PF06732Pescadillo N-terminus (Pescadillo_N)Pescadillo N-terminus- Family
L [auth CJ]PF00533BRCA1 C Terminus (BRCT) domain (BRCT)BRCA1 C Terminus (BRCT) domainThe BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- ...The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs [2]. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilised head-to-tail BRCT-BRCT oligomerisation mode [3]. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants [5].
Domain
K [auth CI]PF00076RNA recognition motif (RRM_1)RNA recognition motifThe RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
Domain
J [auth CH]PF08155NOGCT (NUC087) domain (NOGCT)NOGCT (NUC087) domainThis C terminal domain is found in the NOG subfamily of nucleolar GTP-binding proteins [1]. Domain
J [auth CH]PF06858Nucleolar GTP-binding protein 1 (NOG1) (NOG1)Nucleolar GTP-binding protein 1 (NOG1)- Family
J [auth CH]PF17835NOG1 N-terminal helical domain (NOG1_N)NOG1 N-terminal helical domainThis domain is found at the N-terminus of NOG1 GTPase proteins. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
I [auth CG]60S ribosome subunit biogenesis protein NIP7
H [auth CF]Ribosome assembly factor mrt4
G [auth CE]RNA helicase
F [auth CC]Ribosome biogenesis protein ERB1
CB [auth Cg]Brix domain-containing protein
BB [auth Cf]60S ribosome biogenesis protein Rrp14
AB [auth Ce]Protein MAK16-
ZA [auth Cd]Brix domain-containing protein
YA [auth Cc]Ribosomal RNA-processing protein 1-
E [auth CB]Ribosome biogenesis protein C8F11.04- - -
XA [auth Lq]Ribosomal protein
WA [auth Lj]Ribosomal protein L37
VA [auth Li]60S ribosomal protein L36
UA [auth Lh]dolichyl-diphosphooligosaccharide--protein glycotransferase
TA [auth Lf]60S ribosomal protein l33-like protein
SA [auth Le]60S ribosomal protein L32-like protein
RA [auth LY]60S ribosomal protein L26-like protein
QA [auth LX]60S ribosomal protein L25-like protein
PA [auth LV]60S ribosomal protein l23-like protein
OA [auth LT]60S ribosomal protein l21-like protein
D [auth CA]Brix domain-containing protein
NA [auth LS]60S ribosomal protein L20
MA [auth LQ]Ribosomal protein L18-like protein
LA [auth LP]60S ribosomal protein l17-like protein
KA [auth LO]60S ribosomal protein L16-like protein
JA [auth LN]Ribosomal protein L15
IA [auth LM]60S ribosomal protein L14-like protein
HA [auth LL]60S ribosomal protein L13
GA [auth LK]60S ribosomal protein L12-like protein
FA [auth LH]60S ribosomal protein l9-like protein
EA [auth LG]60S ribosomal protein L8
C [auth C3]RNA (161-MER)---
CA [auth LE]60S ribosomal protein L6
BA [auth LC]60S ribosomal protein L4-like protein
AA [auth LB]60S ribosomal protein L3-like protein
Z [auth Ch]Ribosomal RNA-processing protein 15-
Y [auth Cb]ATP-dependent RNA helicase DBP10
X [auth Cz]rRNA-processing protein-
W [auth CX]60S ribosomal subunit-like protein
V [auth CU]rRNA-processing protein EBP2-
U [auth CS]AdoMet-dependent rRNA methyltransferase SPB1
T [auth CR]Nucleolar protein 16-
B [auth C2]RNA (256-MER)---
S [auth CQ]Ribosome biogenesis protein RLP24
R [auth CP]RNA methyltransferase nop2-like protein
Q [auth CO]DUF2423 domain-containing protein- -
P [auth CN]Eukaryotic translation initiation factor 6
DA [auth LF],
O [auth CM]		60S ribosomal protein l7-like protein
N [auth CL]Putative GTP binding protein
M [auth CK]Ribosome biogenesis protein NSA2 homolog-
L [auth CJ]Pescadillo homolog
K [auth CI]Putative RNA-binding protein -
J [auth CH]Nucleolar GTP-binding protein 1
A [auth C1]RNA (3341-MER)---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
I [auth CG]IPR015947PUA-like superfamilyHomologous Superfamily
I [auth CG]IPR005155UPF0113, PUA domainDomain
I [auth CG]IPR04059860S ribosome subunit biogenesis protein NIP7, pre-PUA domainDomain
I [auth CG]IPR016686Ribosome biogenesis factor, NIP7Family
I [auth CG]IPR002478PUA domainDomain
I [auth CG]IPR036974PUA domain superfamilyHomologous Superfamily
I [auth CG]IPR05535960S ribosome subunit biogenesis protein Nip7, pre-PUA domain, eukaryotesDomain
H [auth CF]IPR043141Large ribosomal subunit protein uL10-like domain superfamilyHomologous Superfamily
H [auth CF]IPR001790Large ribosomal subunit protein uL10Family
H [auth CF]IPR043164Large ribosomal subunit protein uL10-like, insertion domain superfamilyHomologous Superfamily
H [auth CF]IPR051742Ribosomal Assembly Factor uL10Family
H [auth CF]IPR040637Large ribosomal subunit protein uL10-like, insertion domainDomain
H [auth CF]IPR033867Ribosome assembly factor Mrt4Family
G [auth CE]IPR001650Helicase, C-terminal domain-likeDomain
G [auth CE]IPR000629ATP-dependent RNA helicase DEAD-box, conserved siteConserved Site
G [auth CE]IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
G [auth CE]IPR044773DDX18/Has1, DEAD-box helicase domainDomain
G [auth CE]IPR014014RNA helicase, DEAD-box type, Q motifDomain
G [auth CE]IPR025313ATP-dependent rRNA helicase SPB4-like, C-terminal extensionDomain
G [auth CE]IPR011545DEAD/DEAH-box helicase domainDomain
G [auth CE]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
F [auth CC]IPR001680WD40 repeatRepeat
F [auth CC]IPR019775WD40 repeat, conserved siteConserved Site
F [auth CC]IPR012953BOP1, N-terminal domainDomain
F [auth CC]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
F [auth CC]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
F [auth CC]IPR028598WD repeat BOP1/Erb1Family
CB [auth Cg]IPR007109Brix domainDomain
CB [auth Cg]IPR045112Protein Peter Pan-likeFamily
BB [auth Cf]IPR029190Ribosomal RNA-processing protein 14/surfeit locus protein 6, C-terminal domainDomain
BB [auth Cf]IPR029188Ribosomal RNA-processing protein 14, N-terminalDomain
BB [auth Cf]IPR007019Surfeit locus 6Family
AB [auth Ce]IPR006958Mak16 proteinFamily
AB [auth Ce]IPR029004Ribosomal eL28/Mak16Domain
ZA [auth Cd]IPR044281U3 snoRNP protein/Ribosome production factor 1Family
ZA [auth Cd]IPR007109Brix domainDomain
YA [auth Cc]IPR010301Ribosomal RNA processing protein 1Family
E [auth CB]IPR016095Large ribosomal subunit protein uL1, 3-layer alpha/beta-sandwich domainHomologous Superfamily
E [auth CB]IPR023674Ribosomal protein uL1-likeHomologous Superfamily
E [auth CB]IPR028364Ribosomal protein uL1/ribosomal biogenesis proteinFamily
XA [auth Lq]IPR050257Large ribosomal subunit protein eL8/uL1-likeFamily
XA [auth Lq]IPR023673Large ribosomal subunit protein uL1, conserved siteConserved Site
XA [auth Lq]IPR016095Large ribosomal subunit protein uL1, 3-layer alpha/beta-sandwich domainHomologous Superfamily
XA [auth Lq]IPR023674Ribosomal protein uL1-likeHomologous Superfamily
XA [auth Lq]IPR002143Large ribosomal subunit protein uL1Family
XA [auth Lq]IPR028364Ribosomal protein uL1/ribosomal biogenesis proteinFamily
WA [auth Lj]IPR001569Large ribosomal subunit protein eL37Family
WA [auth Lj]IPR018267Large ribosomal subunit protein eL37, conserved siteConserved Site
WA [auth Lj]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
WA [auth Lj]IPR011331Large ribosomal subunit protein eL37/eL43Homologous Superfamily
VA [auth Li]IPR000509Large ribosomal subunit protein eL36Family
VA [auth Li]IPR038097Large ribosomal subunit protein eL36 domain superfamilyHomologous Superfamily
UA [auth Lh]IPR003674Oligosaccharyl transferase, STT3 subunitFamily
UA [auth Lh]IPR048307Oligosaccharyl transferase STT3, N-terminal domainDomain
UA [auth Lh]IPR036049Large ribosomal subunit protein uL29 superfamilyHomologous Superfamily
UA [auth Lh]IPR001854Large ribosomal subunit protein uL29Family
UA [auth Lh]IPR048999STT3/PglB/AglB, core domainDomain
TA [auth Lf]IPR038661Large ribosomal subunit protein eL33 superfamilyHomologous Superfamily
TA [auth Lf]IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
TA [auth Lf]IPR001780Large ribosomal subunit protein eL33Family
TA [auth Lf]IPR018266Large ribosomal subunit protein eL33, conserved siteConserved Site
SA [auth Le]IPR036351Large ribosomal subunit protein eL32 superfamilyHomologous Superfamily
SA [auth Le]IPR001515Large ribosomal subunit protein eL32Family
RA [auth LY]IPR005756Large ribosomal subunit protein uL24, eukaryota_archaeaFamily
RA [auth LY]IPR041988Large ribosomal subunit protein uL24, KOW domainDomain
RA [auth LY]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
RA [auth LY]IPR005824KOWDomain
RA [auth LY]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
QA [auth LX]IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
QA [auth LX]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
QA [auth LX]IPR005633Large ribosomal subunit protein uL23, N-terminalDomain
QA [auth LX]IPR013025Large ribosomal subunit protein uL23-likeFamily
PA [auth LV]IPR036853Large ribosomal subunit protein uL14 superfamilyHomologous Superfamily
PA [auth LV]IPR000218Large ribosomal subunit protein uL14Family
PA [auth LV]IPR019972Large ribosomal subunit protein uL14, conserved siteConserved Site
OA [auth LT]IPR018259Large ribosomal subunit protein eL21, conserved siteConserved Site
OA [auth LT]IPR036948Large ribosomal subunit protein eL21 superfamilyHomologous Superfamily
OA [auth LT]IPR001147Large ribosomal subunit protein eL21Family
OA [auth LT]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
D [auth CA]IPR026532Ribosome biogenesis protein BRX1Family
D [auth CA]IPR007109Brix domainDomain
NA [auth LS]IPR028877Large ribosomal subunit protein eL20Family
NA [auth LS]IPR023573Large ribosomal subunit protein eL20 domainDomain
NA [auth LS]IPR021138Large ribosomal subunit protein eL20, eukaryotaFamily
MA [auth LQ]IPR021131Large ribosomal subunit protein uL15/eL18Domain
MA [auth LQ]IPR021132Large ribosomal subunit protein eL18, conserved siteConserved Site
MA [auth LQ]IPR000039Large ribosomal subunit protein eL18Family
MA [auth LQ]IPR036227Large ribosomal subunit protein uL15/eL18 superfamilyHomologous Superfamily
LA [auth LP]IPR018260Large ribosomal subunit protein uL22, conserved siteConserved Site
LA [auth LP]IPR005721Large ribosomal subunit protein uL22, eukaryota/archaeaFamily
LA [auth LP]IPR036394Ribosomal protein uL22 superfamilyHomologous Superfamily
LA [auth LP]IPR001063Large ribosomal subunit protein uL22Family
KA [auth LO]IPR023563Large ribosomal subunit protein uL13, conserved siteConserved Site
KA [auth LO]IPR005822Large ribosomal subunit protein uL13Family
KA [auth LO]IPR036899Large ribosomal subunit protein uL13 superfamilyHomologous Superfamily
KA [auth LO]IPR005755Large ribosomal subunit protein uL13, eukaryota/archaeaFamily
JA [auth LN]IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
JA [auth LN]IPR020925Large ribosomal subunit protein eL15, conserved siteConserved Site
JA [auth LN]IPR024794Large ribosomal subunit protein eL15 core domain superfamilyHomologous Superfamily
JA [auth LN]IPR000439Large ribosomal subunit protein eL15Family
IA [auth LM]IPR039660Large ribosomal subunit protein eL14Family
IA [auth LM]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
IA [auth LM]IPR002784Large ribosomal subunit protein eL14 domainDomain
IA [auth LM]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
HA [auth LL]IPR001380Large ribosomal subunit protein eL13Family
HA [auth LL]IPR018256Large ribosomal subunit protein eL13, conserved siteConserved Site
GA [auth LK]IPR020785Large ribosomal subunit protein uL11, conserved siteConserved Site
GA [auth LK]IPR020783Large ribosomal subunit protein uL11, C-terminalDomain
GA [auth LK]IPR000911Ribosomal protein uL11Family
GA [auth LK]IPR036769Large ribosomal subunit protein uL11, C-terminal domain superfamilyHomologous Superfamily
GA [auth LK]IPR020784Large ribosomal subunit protein uL11, N-terminalDomain
GA [auth LK]IPR036796Large ribosomal subunit protein uL11, N-terminal domain superfamilyHomologous Superfamily
FA [auth LH]IPR020040Large ribosomal subunit protein uL6, alpha-beta domainDomain
FA [auth LH]IPR002359Large ribosomal subunit protein uL6, conserved site-2Conserved Site
FA [auth LH]IPR036789Large ribosomal subunit protein uL6-like, alpha-beta domain superfamilyHomologous Superfamily
FA [auth LH]IPR000702Large ribosomal subunit protein uL6-likeFamily
EA [auth LG]IPR050257Large ribosomal subunit protein eL8/uL1-likeFamily
EA [auth LG]IPR004038Ribosomal protein eL8/eL30/eS12/Gadd45Domain
EA [auth LG]IPR004037Large ribosomal subunit protein eL8-like, conserved siteConserved Site
EA [auth LG]IPR029064Ribosomal protein eL30-like superfamilyHomologous Superfamily
EA [auth LG]IPR018492Ribosomal protein eL8/Nhp2 familyFamily
EA [auth LG]IPR001921Large ribosomal subunit protein eL8, eukaryotaFamily
CA [auth LE]IPR049633Large ribosomal subunit protein eL6, conserved siteConserved Site
CA [auth LE]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
CA [auth LE]IPR041997Large ribosomal subunit protein eL6, KOW domainDomain
CA [auth LE]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
CA [auth LE]IPR000915Large ribosomal subunit protein eL6Family
BA [auth LC]IPR025755Large ribosomal subunit protein uL4, C-terminal domainDomain
BA [auth LC]IPR002136Large ribosomal subunit protein uL4Family
BA [auth LC]IPR013000Large ribosomal subunit protein uL4, eukaryota/archaea, conserved siteConserved Site
BA [auth LC]IPR045240Large ribosomal subunit protein uL4, eukaryota/archaeaFamily
BA [auth LC]IPR023574Large ribosomal subunit protein uL4 domain superfamilyHomologous Superfamily
AA [auth LB]IPR019926Large ribosomal subunit protein uL3, conserved siteConserved Site
AA [auth LB]IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
AA [auth LB]IPR044892Ribosomal protein L3, domain 3, archaeal-type superfamilyHomologous Superfamily
AA [auth LB]IPR000597Large ribosomal subunit protein uL3Family
AA [auth LB]IPR045077Large ribosomal subunit protein uL3, archaea/eukaryotaFamily
Z [auth Ch]IPR012459Ribosomal RNA-processing protein 15Family
Y [auth Cb]IPR001650Helicase, C-terminal domain-likeDomain
Y [auth Cb]IPR000629ATP-dependent RNA helicase DEAD-box, conserved siteConserved Site
Y [auth Cb]IPR050079DEAD box RNA helicaseFamily
Y [auth Cb]IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
Y [auth Cb]IPR012541DBP10, C-terminalDomain
Y [auth Cb]IPR033517DDX54/DBP10 family, DEAD-box helicase domainDomain
Y [auth Cb]IPR014014RNA helicase, DEAD-box type, Q motifDomain
Y [auth Cb]IPR011545DEAD/DEAH-box helicase domainDomain
Y [auth Cb]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
X [auth Cz]IPR005579Cgr1-likeFamily
W [auth CX]IPR03765060S ribosomal subunit assembly/export protein Loc1Family
V [auth CU]IPR008610Eukaryotic rRNA processingFamily
U [auth CS]IPR024576Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381Domain
U [auth CS]IPR012920Ribosomal RNA methyltransferase, SPB1-like, C-terminalDomain
U [auth CS]IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
U [auth CS]IPR002877Ribosomal RNA methyltransferase, FtsJ domainDomain
U [auth CS]IPR015507Ribosomal RNA large subunit methyltransferase EFamily
U [auth CS]IPR028589AdoMet-dependent rRNA methyltransferase SPB1-likeFamily
U [auth CS]IPR050082Ribosomal RNA large subunit methyltransferase RlmEFamily
T [auth CR]IPR019002Ribosome biogenesis protein Nop16Family
S [auth CQ]IPR011017TRASH domainDomain
S [auth CQ]IPR056366Large ribosomal subunit protein eL24Family
S [auth CQ]IPR000988Large ribosomal subunit protein eL24-related, N-terminalDomain
S [auth CQ]IPR038630Ribosomal protein L24e/L24 superfamilyHomologous Superfamily
R [auth CP]IPR054728Ribosomal RNA small subunit methyltransferase B-like, ferredoxin-like domainDomain
R [auth CP]IPR018314RsmB/NOL1/NOP2-like, conserved siteConserved Site
R [auth CP]IPR001678SAM-dependent methyltransferase RsmB-F/NOP2-type domainDomain
R [auth CP]IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
R [auth CP]IPR023267RNA (C5-cytosine) methyltransferaseFamily
R [auth CP]IPR011023Nop2pDomain
R [auth CP]IPR023273RNA (C5-cytosine) methyltransferase, NOP2Family
R [auth CP]IPR049560SAM-dependent methyltransferase RsmB-F/NOP2-type, catalytic coreDomain
Q [auth CO]IPR019434Domain of unknown function DUF2423Domain
P [auth CN]IPR002769Translation initiation factor IF6Family
DA [auth LF],
O [auth CM]		IPR036919Large ribosomal subunit protein uL30, ferredoxin-like fold domain superfamilyHomologous Superfamily
DA [auth LF],
O [auth CM]		IPR005998Large ribosomal subunit protein uL30, eukaryotaFamily
DA [auth LF],
O [auth CM]		IPR039699Large ribosomal subunit protein uL30Family
DA [auth LF],
O [auth CM]		IPR035808Large ribosomal subunit protein uL30, eukaryota/archaeaDomain
DA [auth LF],
O [auth CM]		IPR012988Large ribosomal subunit protein uL30, N-terminal, eukaryotaDomain
DA [auth LF],
O [auth CM]		IPR016082Large ribosomal subunit protein uL30-like, ferredoxin-like fold domainDomain
N [auth CL]IPR050755TRAFAC YlqF/YawG GTPases, Ribosome MaturationFamily
N [auth CL]IPR030378Circularly permuted (CP)-type guanine nucleotide-binding (G) domainDomain
N [auth CL]IPR006073GTP binding domainDomain
N [auth CL]IPR014813Guanine nucleotide-binding protein-like 3, N-terminal domainDomain
N [auth CL]IPR023179GTP-binding protein, orthogonal bundle domain superfamilyHomologous Superfamily
N [auth CL]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
M [auth CK]IPR039411Ribosomal biogenesis NSA2 familyFamily
M [auth CK]IPR022309Ribosomal protein eS8/ribosomal biogenesis NSA2Family
L [auth CJ]IPR001357BRCT domainDomain
L [auth CJ]IPR010613PescadilloFamily
L [auth CJ]IPR036420BRCT domain superfamilyHomologous Superfamily
K [auth CI]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
K [auth CI]IPR000504RNA recognition motif domainDomain
K [auth CI]IPR035979RNA-binding domain superfamilyHomologous Superfamily
J [auth CH]IPR024926Nucleolar GTP-binding protein 1Family
J [auth CH]IPR031167OBG-type guanine nucleotide-binding (G) domainDomain
J [auth CH]IPR012973NOG, C-terminalDomain
J [auth CH]IPR041623NOG1, N-terminal helical domainDomain
J [auth CH]IPR006073GTP binding domainDomain
J [auth CH]IPR010674Nucleolar GTP-binding protein 1, Rossman-fold domainDomain
J [auth CH]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily