6ND4

Conformational switches control early maturation of the eukaryotic small ribosomal subunit


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
N [auth R]SCOP2B SuperfamilyUTPB complex component-like8061270 3002330 SCOP2B (2022-06-29)
X [auth c]SCOP2B SuperfamilyS-adenosyl-L-methionine-dependent methyltransferases8063662 3000118 SCOP2B (2022-06-29)
Y [auth d]SCOP2B SuperfamilyS-adenosyl-L-methionine-dependent methyltransferases8063662 3000118 SCOP2B (2022-06-29)
AA [auth f]SCOP2B SuperfamilyL30e-like8033484 3001739 SCOP2B (2022-06-29)
Z [auth e]SCOP2B SuperfamilyL30e-like8033484 3001739 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
H [auth L]F_UNCLASSIFIEDe6nd4L1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 8-bladedF: F_UNCLASSIFIEDECOD (1.6)
H [auth L]PF04003e6nd4L2 A: alpha superhelicesX: Repetitive alpha hairpinsH: C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 (From Topology)T: C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13F: PF04003ECOD (1.6)
I [auth M]PF12397e6nd4M1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: PF12397ECOD (1.6)
J [auth N]F_UNCLASSIFIEDe6nd4N2 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: F_UNCLASSIFIEDECOD (1.6)
J [auth N]PF00400e6nd4N1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
K [auth O]PF00400e6nd4O1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
K [auth O]PF04003e6nd4O2 A: alpha superhelicesX: Repetitive alpha hairpinsH: C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 (From Topology)T: C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13F: PF04003ECOD (1.6)
M [auth Q]PF00400e6nd4Q2 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
M [auth Q]PF04003e6nd4Q3 A: alpha superhelicesX: Repetitive alpha hairpinsH: C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 (From Topology)T: C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13F: PF04003ECOD (1.6)
P [auth T]PF00400e6nd4T1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
P [auth T]PF12894e6nd4T3 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF12894ECOD (1.6)
P [auth T]PF04192e6nd4T2 A: alpha superhelicesX: Repetitive alpha hairpinsH: C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 (From Topology)T: C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13F: PF04192ECOD (1.6)
Q [auth U]PF00400e6nd4U1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
R [auth W]PF00400,PF08149e6nd4W1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 8-bladedF: PF00400,PF08149ECOD (1.6)
V [auth a]PF01798e6nd4a1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: Nop C-terminal domainF: PF01798ECOD (1.6)
V [auth a]PF01798e6nd4a3 A: alpha complex topologyX: Nop N-terminal domain (From Topology)H: Nop N-terminal domain (From Topology)T: Nop N-terminal domainF: PF01798ECOD (1.6)
V [auth a]PF08156e6nd4a2 A: mixed a+b and a/bX: Nop N-terminal domain (From Topology)H: Nop N-terminal domain (From Topology)T: Nop N-terminal domainF: PF08156ECOD (1.6)
X [auth c]PF01269e6nd4c1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: S-adenosyl-L-methionine-dependent methyltransferasesF: PF01269ECOD (1.6)
Y [auth d]PF01269e6nd4d1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: S-adenosyl-L-methionine-dependent methyltransferasesF: PF01269ECOD (1.6)
AA [auth f]PF01248e6nd4f1 A: a+b three layersX: Bacillus chorismate mutase-likeH: L30e-like (From Topology)T: L30e-likeF: PF01248ECOD (1.6)
Z [auth e]PF01248e6nd4e1 A: a+b three layersX: Bacillus chorismate mutase-likeH: L30e-like (From Topology)T: L30e-likeF: PF01248ECOD (1.6)
BA [auth g]PF00400e6nd4g1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
D [auth H]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
H [auth L]PF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
I [auth M]PF12397U3 small nucleolar RNA-associated protein 10 (U3snoRNP10)U3 small nucleolar RNA-associated protein 10- Family
J [auth N]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
K [auth O]PF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
K [auth O]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
L [auth P]PF08640U3 small nucleolar RNA-associated protein 6 (U3_assoc_6)U3 small nucleolar RNA-associated protein 6- Family
M [auth Q]PF04003Dip2/Utp12 Family (Utp12)Dip2/Utp12 Family- Family
M [auth Q]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
N [auth R]PF08625Utp13 specific WD40 associated domain (Utp13)Utp13 specific WD40 associated domainUtp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome [1]. Pwp2 is capable o ...Utp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome [1]. Pwp2 is capable of interacting directly with the 35 S pre-rRNA 5' end [1].
Domain
O [auth S]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
P [auth T]PF04192Utp21 specific WD40 associated putative domain (Utp21)Utp21 specific WD40 associated putative domainUtp21 is a subunit of U3 snoRNP, which is essential for synthesis of 18S rRNA.Domain
P [auth T]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
Q [auth U]PF04158Sof1-like domain (Sof1)Sof1-like domain- Family
Q [auth U]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
R [auth W]PF08149BING4CT (NUC141) domain (BING4CT)BING4CT (NUC141) domainThis C terminal domain is found in the BING4 family of nucleolar WD40 repeat proteins [1].Domain
R [auth W]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
S [auth Z]PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
S [auth Z]PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
T [auth A]PF04006Mpp10 protein (Mpp10)Mpp10 protein- Family
U [auth D]PF08297U3 snoRNA associated (U3_snoRNA_assoc)U3 snoRNA associated- Family
V [auth a]PF08156NOP5NT (NUC127) domain (NOP5NT)NOP5NT (NUC127) domainThis N terminal domain is found in RNA-binding proteins of the NOP5 family [1].Domain
V [auth a]PF01798snoRNA binding domain, fibrillarin (Nop)snoRNA binding domain, fibrillarin- Family
W [auth b]PF01798snoRNA binding domain, fibrillarin (Nop)snoRNA binding domain, fibrillarin- Family
X [auth c],
Y [auth d]
PF01269Fibrillarin (Fibrillarin)Fibrillarin- Domain
AA [auth f],
Z [auth e]
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
BA [auth g]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
E [auth I]PF10395Utp8 family (Utp8)Utp8 family- Family
F [auth J]PF09384UTP15 C terminal (UTP15_C)UTP15 C terminal- Family
F [auth J]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth 0]5'ETS rRNA---
B [auth 1]18S rRNA 5' domain start---
C [auth 2]U3 snoRNA---
D [auth H]Utp17
H [auth L]Utp5-
I [auth M]Utp10
J [auth N]Utp4-
K [auth O]Utp1
L [auth P]Utp6
M [auth Q]Utp12
N [auth R]Utp13
O [auth S]Utp18-
P [auth T]Utp21-
Q [auth U]Sof1
R [auth W]Utp7-
S [auth Z]Imp3
T [auth A]Mpp10
U [auth D]Bud21
V [auth a]Nop56
W [auth b]Nop58
X [auth c],
Y [auth d]
Nop1.1
AA [auth f],
Z [auth e]
Snu13
CA [auth l]Utp24
DA [auth x]Unidentified fragment---
BA [auth g]Rrp9
E [auth I]Utp8
F [auth J]Utp15
G [auth K]Utp9

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
D [auth H]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
D [auth H]IPR001680WD40 repeatRepeat
D [auth H]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
H [auth L]IPR007148Small-subunit processome, Utp12Domain
H [auth L]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
H [auth L]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
I [auth M]IPR016024Armadillo-type foldHomologous Superfamily
I [auth M]IPR040191U3 small nucleolar RNA-associated protein 10Family
I [auth M]IPR021133HEAT, type 2Repeat
I [auth M]IPR011989Armadillo-like helicalHomologous Superfamily
I [auth M]IPR022125U3 small nucleolar RNA-associated protein 10, N-terminalDomain
I [auth M]IPR012954BP28, C-terminal domainDomain
J [auth N]IPR001680WD40 repeatRepeat
J [auth N]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
J [auth N]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
K [auth O]IPR024977Anaphase-promoting complex subunit 4-like, WD40 domainDomain
K [auth O]IPR019775WD40 repeat, conserved siteConserved Site
K [auth O]IPR007148Small-subunit processome, Utp12Domain
K [auth O]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
K [auth O]IPR011047Quinoprotein alcohol dehydrogenase-like superfamilyHomologous Superfamily
K [auth O]IPR001680WD40 repeatRepeat
K [auth O]IPR020472G-protein beta WD-40 repeatRepeat
K [auth O]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
K [auth O]IPR027145Periodic tryptophan protein 2Family
L [auth P]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
L [auth P]IPR003107HAT (Half-A-TPR) repeatRepeat
L [auth P]IPR013949U3 small nucleolar RNA-associated protein 6Family
M [auth Q]IPR019775WD40 repeat, conserved siteConserved Site
M [auth Q]IPR007148Small-subunit processome, Utp12Domain
M [auth Q]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
M [auth Q]IPR001680WD40 repeatRepeat
M [auth Q]IPR020472G-protein beta WD-40 repeatRepeat
M [auth Q]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
N [auth R]IPR019775WD40 repeat, conserved siteConserved Site
N [auth R]IPR013934U3 small nucleolar RNA-associated protein 13, C-terminalDomain
N [auth R]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
N [auth R]IPR001680WD40 repeatRepeat
N [auth R]IPR020472G-protein beta WD-40 repeatRepeat
N [auth R]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
O [auth S]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
O [auth S]IPR001680WD40 repeatRepeat
O [auth S]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
O [auth S]IPR045161U3 small nucleolar RNA-associated protein 18Family
P [auth T]IPR007319Small-subunit processome, Utp21Domain
P [auth T]IPR024977Anaphase-promoting complex subunit 4-like, WD40 domainDomain
P [auth T]IPR019775WD40 repeat, conserved siteConserved Site
P [auth T]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
P [auth T]IPR011047Quinoprotein alcohol dehydrogenase-like superfamilyHomologous Superfamily
P [auth T]IPR001680WD40 repeatRepeat
P [auth T]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
Q [auth U]IPR001680WD40 repeatRepeat
Q [auth U]IPR007287Sof1-like proteinDomain
Q [auth U]IPR020472G-protein beta WD-40 repeatRepeat
Q [auth U]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
Q [auth U]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
R [auth W]IPR019775WD40 repeat, conserved siteConserved Site
R [auth W]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
R [auth W]IPR012952BING4, C-terminal domainDomain
R [auth W]IPR001680WD40 repeatRepeat
R [auth W]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
R [auth W]IPR040315WD repeat-containing protein WDR46/Utp7Family
S [auth Z]IPR002942RNA-binding S4 domainDomain
S [auth Z]IPR022801Small ribosomal subunit protein uS4Family
S [auth Z]IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
S [auth Z]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
T [auth A]IPR012173U3 small nucleolar ribonucleoprotein complex, subunit Mpp10Family
U [auth D]IPR013268U3 small nucleolar RNA-associated protein 16Family
V [auth a]IPR042239Nop, C-terminal domainHomologous Superfamily
V [auth a]IPR012974Nucleolar protein 58/56, N-terminalDomain
V [auth a]IPR002687Nop domainDomain
V [auth a]IPR012976NOSICDomain
V [auth a]IPR036070Nop domain superfamilyHomologous Superfamily
V [auth a]IPR045056Nucleolar protein Nop56/Nop58Family
W [auth b]IPR042239Nop, C-terminal domainHomologous Superfamily
W [auth b]IPR012974Nucleolar protein 58/56, N-terminalDomain
W [auth b]IPR002687Nop domainDomain
W [auth b]IPR012976NOSICDomain
W [auth b]IPR036070Nop domain superfamilyHomologous Superfamily
W [auth b]IPR045056Nucleolar protein Nop56/Nop58Family
X [auth c],
Y [auth d]
IPR000692rRNA 2'-O-methyltransferase fibrillarin-likeFamily
X [auth c],
Y [auth d]
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
X [auth c],
Y [auth d]
IPR020813Fibrillarin, conserved siteConserved Site
AA [auth f],
Z [auth e]
IPR002415H/ACA ribonucleoprotein complex, subunit Nhp2-likeFamily
AA [auth f],
Z [auth e]
IPR029064Ribosomal protein eL30-like superfamilyHomologous Superfamily
AA [auth f],
Z [auth e]
IPR018492Ribosomal protein eL8/Nhp2 familyFamily
AA [auth f],
Z [auth e]
IPR004038Ribosomal protein eL8/eL30/eS12/Gadd45Domain
AA [auth f],
Z [auth e]
IPR004037Large ribosomal subunit protein eL8-like, conserved siteConserved Site
CA [auth l]IPR002716PIN domainDomain
CA [auth l]IPR029060PIN-like domain superfamilyHomologous Superfamily
CA [auth l]IPR006984rRNA-processing protein Fcf1/Utp23Family
CA [auth l]IPR037503rRNA-processing protein Fcf1, PIN domainDomain
BA [auth g]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
BA [auth g]IPR039241Ribosomal RNA-processing protein Rrp9-likeFamily
BA [auth g]IPR001680WD40 repeatRepeat
BA [auth g]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
E [auth I]IPR018843U3 small nucleolar RNA-associated protein 8Family
F [auth J]IPR019775WD40 repeat, conserved siteConserved Site
F [auth J]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
F [auth J]IPR001680WD40 repeatRepeat
F [auth J]IPR018983U3 small nucleolar RNA-associated protein 15, C-terminalDomain
F [auth J]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
G [auth K]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily