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Protein

Ribosome maturation protein SBDS

Gene

SBDS

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Required for the assembly of mature ribosomes and ribosome biogenesis. Together with EFL1, triggers the GTP-dependent release of EIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating EIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. Required for normal levels of protein synthesis. May play a role in cellular stress resistance. May play a role in cellular response to DNA damage. May play a role in cell proliferation.4 Publications

GO - Molecular functioni

  • microtubule binding Source: UniProtKB
  • ribosome binding Source: UniProtKB
  • RNA binding Source: UniProtKB
  • rRNA binding Source: UniProtKB

GO - Biological processi

Keywordsi

Biological processRibosome biogenesis

Enzyme and pathway databases

SIGNORiQ9Y3A5

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosome maturation protein SBDS
Alternative name(s):
Shwachman-Bodian-Diamond syndrome protein
Gene namesi
Name:SBDS
ORF Names:CGI-97
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

EuPathDBiHostDB:ENSG00000126524.9
HGNCiHGNC:19440 SBDS
MIMi607444 gene
neXtProtiNX_Q9Y3A5

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton, Nucleus

Pathology & Biotechi

Involvement in diseasei

Shwachman-Diamond syndrome (SDS)3 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAutosomal recessive disorder characterized by pancreatic exocrine insufficiency, hematologic dysfunction, and skeletal abnormalities.
See also OMIM:260400
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0153908N → K in SDS; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs28942099EnsemblClinVar.1
Natural variantiVAR_07167333K → T in SDS. 1 PublicationCorresponds to variant dbSNP:rs373730800EnsemblClinVar.1
Natural variantiVAR_01539144E → G in SDS; unknown pathological significance. 1 Publication1
Natural variantiVAR_01539267K → E in SDS; unknown pathological significance. 1 Publication1
Natural variantiVAR_01539387I → S in SDS; unknown pathological significance. 1 Publication1
Natural variantiVAR_015394126R → T in SDS; strongly reduced release of EIF6 from pre-60S ribosome subunits. 2 PublicationsCorresponds to variant dbSNP:rs113993995EnsemblClinVar.1
Natural variantiVAR_015395169R → C in SDS; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs113993996EnsemblClinVar.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi151K → N: Strongly reduced release of EIF6 from pre-60S ribosome subunits. 1 Publication1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi51119
GeneReviewsiSBDS
MalaCardsiSBDS
MIMi260400 phenotype
OpenTargetsiENSG00000126524
Orphaneti88 Idiopathic aplastic anemia
811 Shwachman-Diamond syndrome
PharmGKBiPA134978742

Polymorphism and mutation databases

BioMutaiSBDS
DMDMi28380824

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00001237622 – 250Ribosome maturation protein SBDSAdd BLAST249

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1 Publication1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9Y3A5
MaxQBiQ9Y3A5
PaxDbiQ9Y3A5
PeptideAtlasiQ9Y3A5
PRIDEiQ9Y3A5
ProteomicsDBi85997

PTM databases

iPTMnetiQ9Y3A5
PhosphoSitePlusiQ9Y3A5

Expressioni

Tissue specificityi

Widely expressed.

Gene expression databases

BgeeiENSG00000126524 Expressed in 97 organ(s), highest expression level in tibial artery
CleanExiHS_SBDS
ExpressionAtlasiQ9Y3A5 baseline and differential
GenevisibleiQ9Y3A5 HS

Organism-specific databases

HPAiHPA028891

Interactioni

Subunit structurei

Associates with the 60S ribosomal subunit. Interacts with NPM1, RPA1 and PRKDC. May interact with NIP7 (PubMed:17643419). Found in a complex consisting of the 60S ribosomal subunit, SBDS and EFL1 (PubMed:26479198). Interacts with EFL1 (PubMed:25991726).5 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi119307, 62 interactors
IntActiQ9Y3A5, 7 interactors
STRINGi9606.ENSP00000246868

Structurei

Secondary structure

1250
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ9Y3A5
SMRiQ9Y3A5
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y3A5

Family & Domainsi

Sequence similaritiesi

Belongs to the SDO1/SBDS family.Curated

Phylogenomic databases

eggNOGiKOG2917 Eukaryota
COG1500 LUCA
GeneTreeiENSGT00390000008135
HOGENOMiHOG000216685
HOVERGENiHBG039762
InParanoidiQ9Y3A5
KOiK14574
OMAiAVNPQMD
PhylomeDBiQ9Y3A5
TreeFamiTF300881

Family and domain databases

Gene3Di1.10.10.900, 1 hit
3.30.1250.10, 1 hit
InterProiView protein in InterPro
IPR018978 Ribosome_mat_SBDS_C
IPR018023 Ribosome_mat_SBDS_CS
IPR019783 Ribosome_mat_SBDS_N
IPR036786 Ribosome_mat_SBDS_N_sf
IPR002140 Sdo1/SBDS
IPR039100 Sdo1/SBDS-like
IPR037188 Sdo1/SBDS_central_sf
PANTHERiPTHR10927 PTHR10927, 1 hit
PTHR10927:SF1 PTHR10927:SF1, 1 hit
PfamiView protein in Pfam
PF01172 SBDS, 1 hit
PF09377 SBDS_C, 1 hit
SUPFAMiSSF109728 SSF109728, 1 hit
SSF89895 SSF89895, 1 hit
TIGRFAMsiTIGR00291 RNA_SBDS, 1 hit
PROSITEiView protein in PROSITE
PS01267 UPF0023, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.iShow all

Q9Y3A5-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSIFTPTNQI RLTNVAVVRM KRAGKRFEIA CYKNKVVGWR SGVEKDLDEV
60 70 80 90 100
LQTHSVFVNV SKGQVAKKED LISAFGTDDQ TEICKQILTK GEVQVSDKER
110 120 130 140 150
HTQLEQMFRD IATIVADKCV NPETKRPYTV ILIERAMKDI HYSVKTNKST
160 170 180 190 200
KQQALEVIKQ LKEKMKIERA HMRLRFILPV NEGKKLKEKL KPLIKVIESE
210 220 230 240 250
DYGQQLEIVC LIDPGCFREI DELIKKETKG KGSLEVLNLK DVEEGDEKFE
Length:250
Mass (Da):28,764
Last modified:January 23, 2007 - v4
Checksum:iD35C43003C05F5A7
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A087X020A0A087X020_HUMAN
Ribosome maturation protein SBDS
SBDS
250Annotation score:
F8WE72F8WE72_HUMAN
Ribosome maturation protein SBDS
SBDS
86Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti41 – 43SGV → RAW in AAD34092 (PubMed:10810093).Curated3
Sequence conflicti89T → A in AAD34092 (PubMed:10810093).Curated1
Sequence conflicti105E → G in AAD34092 (PubMed:10810093).Curated1
Sequence conflicti114I → F in AAD34092 (PubMed:10810093).Curated1
Sequence conflicti126R → G in AAD34092 (PubMed:10810093).Curated1
Sequence conflicti143S → L in AAD34092 (PubMed:10810093).Curated1
Sequence conflicti146T → P in AAD34092 (PubMed:10810093).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0153908N → K in SDS; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs28942099EnsemblClinVar.1
Natural variantiVAR_07167333K → T in SDS. 1 PublicationCorresponds to variant dbSNP:rs373730800EnsemblClinVar.1
Natural variantiVAR_01539144E → G in SDS; unknown pathological significance. 1 Publication1
Natural variantiVAR_01539267K → E in SDS; unknown pathological significance. 1 Publication1
Natural variantiVAR_01539387I → S in SDS; unknown pathological significance. 1 Publication1
Natural variantiVAR_015394126R → T in SDS; strongly reduced release of EIF6 from pre-60S ribosome subunits. 2 PublicationsCorresponds to variant dbSNP:rs113993995EnsemblClinVar.1
Natural variantiVAR_015395169R → C in SDS; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs113993996EnsemblClinVar.1
Natural variantiVAR_015396212I → T1 PublicationCorresponds to variant dbSNP:rs79344818EnsemblClinVar.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY169963 mRNA Translation: AAN77490.1
AF151855 mRNA Translation: AAD34092.1
AK001779 mRNA Translation: BAA91905.1
AK289609 mRNA Translation: BAF82298.1
CH471140 Genomic DNA Translation: EAX07906.1
BC065700 mRNA Translation: AAH65700.1
CCDSiCCDS5537.1
RefSeqiNP_057122.2, NM_016038.3
UniGeneiHs.110445

Genome annotation databases

EnsembliENST00000246868; ENSP00000246868; ENSG00000126524
GeneIDi51119
KEGGihsa:51119
UCSCiuc003tvm.2 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Web resourcesi

SBDSbase

SBDS mutation db

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY169963 mRNA Translation: AAN77490.1
AF151855 mRNA Translation: AAD34092.1
AK001779 mRNA Translation: BAA91905.1
AK289609 mRNA Translation: BAF82298.1
CH471140 Genomic DNA Translation: EAX07906.1
BC065700 mRNA Translation: AAH65700.1
CCDSiCCDS5537.1
RefSeqiNP_057122.2, NM_016038.3
UniGeneiHs.110445

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KDONMR-A1-250[»]
2L9NNMR-A1-250[»]
5AN9electron microscopy3.30J1-250[»]
5ANBelectron microscopy4.10J1-250[»]
5ANCelectron microscopy4.20J1-250[»]
ProteinModelPortaliQ9Y3A5
SMRiQ9Y3A5
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119307, 62 interactors
IntActiQ9Y3A5, 7 interactors
STRINGi9606.ENSP00000246868

PTM databases

iPTMnetiQ9Y3A5
PhosphoSitePlusiQ9Y3A5

Polymorphism and mutation databases

BioMutaiSBDS
DMDMi28380824

Proteomic databases

EPDiQ9Y3A5
MaxQBiQ9Y3A5
PaxDbiQ9Y3A5
PeptideAtlasiQ9Y3A5
PRIDEiQ9Y3A5
ProteomicsDBi85997

Protocols and materials databases

DNASUi51119
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000246868; ENSP00000246868; ENSG00000126524
GeneIDi51119
KEGGihsa:51119
UCSCiuc003tvm.2 human

Organism-specific databases

CTDi51119
DisGeNETi51119
EuPathDBiHostDB:ENSG00000126524.9
GeneCardsiSBDS
GeneReviewsiSBDS
HGNCiHGNC:19440 SBDS
HPAiHPA028891
MalaCardsiSBDS
MIMi260400 phenotype
607444 gene
neXtProtiNX_Q9Y3A5
OpenTargetsiENSG00000126524
Orphaneti88 Idiopathic aplastic anemia
811 Shwachman-Diamond syndrome
PharmGKBiPA134978742
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2917 Eukaryota
COG1500 LUCA
GeneTreeiENSGT00390000008135
HOGENOMiHOG000216685
HOVERGENiHBG039762
InParanoidiQ9Y3A5
KOiK14574
OMAiAVNPQMD
PhylomeDBiQ9Y3A5
TreeFamiTF300881

Enzyme and pathway databases

SIGNORiQ9Y3A5

Miscellaneous databases

ChiTaRSiSBDS human
EvolutionaryTraceiQ9Y3A5
GeneWikiiSBDS
GenomeRNAii51119
PROiPR:Q9Y3A5
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000126524 Expressed in 97 organ(s), highest expression level in tibial artery
CleanExiHS_SBDS
ExpressionAtlasiQ9Y3A5 baseline and differential
GenevisibleiQ9Y3A5 HS

Family and domain databases

Gene3Di1.10.10.900, 1 hit
3.30.1250.10, 1 hit
InterProiView protein in InterPro
IPR018978 Ribosome_mat_SBDS_C
IPR018023 Ribosome_mat_SBDS_CS
IPR019783 Ribosome_mat_SBDS_N
IPR036786 Ribosome_mat_SBDS_N_sf
IPR002140 Sdo1/SBDS
IPR039100 Sdo1/SBDS-like
IPR037188 Sdo1/SBDS_central_sf
PANTHERiPTHR10927 PTHR10927, 1 hit
PTHR10927:SF1 PTHR10927:SF1, 1 hit
PfamiView protein in Pfam
PF01172 SBDS, 1 hit
PF09377 SBDS_C, 1 hit
SUPFAMiSSF109728 SSF109728, 1 hit
SSF89895 SSF89895, 1 hit
TIGRFAMsiTIGR00291 RNA_SBDS, 1 hit
PROSITEiView protein in PROSITE
PS01267 UPF0023, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSBDS_HUMAN
AccessioniPrimary (citable) accession number: Q9Y3A5
Secondary accession number(s): A8K0P4, Q96FX0, Q9NV53
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 23, 2007
Last modified: September 12, 2018
This is version 173 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome
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Main funding by: National Institutes of Health

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