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Q9Y3A5 (SBDS_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 127. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribosome maturation protein SBDS
Alternative name(s):
Shwachman-Bodian-Diamond syndrome protein
Gene names
Name:SBDS
ORF Names:CGI-97
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length250 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Required for the assembly of mature ribosomes and ribosome biogenesis. Together with EFTUD1, 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. Ref.9 Ref.10 Ref.11 Ref.16

Subunit structure

Associates with the 60S ribosomal subunit. Interacts with NPM1, RPA1 and PRKDC. May interact with NIP7. Ref.8 Ref.9 Ref.10

Subcellular location

Cytoplasm. Nucleusnucleolus. Nucleusnucleoplasm. Cytoplasmcytoskeletonspindle. Note: Primarily detected in the cytoplasm, and at low levels in nucleus and nucleolus (Ref.10 and Ref.8). Detected in the nucleolus during G1 and G2 phase of the cell cycle, and diffusely distributed in the nucleus during S phase. Detected at the mitotic spindle. Colocalizes with the microtubule organizing center during interphase (Ref.11). Ref.7 Ref.8 Ref.10 Ref.11

Tissue specificity

Widely expressed.

Involvement in disease

Shwachman-Diamond syndrome (SDS) [MIM:260400]: Autosomal recessive disorder characterized by pancreatic exocrine insufficiency, hematologic dysfunction, and skeletal abnormalities.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.1 Ref.16

Sequence similarities

Belongs to the SDO1/SBDS family.

Ontologies

Keywords
   Biological processRibosome biogenesis
   Cellular componentCytoplasm
Cytoskeleton
Nucleus
   DiseaseDisease mutation
   PTMAcetylation
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processbone marrow development

Inferred from mutant phenotype PubMed 15342903. Source: UniProtKB

bone mineralization

Inferred from mutant phenotype PubMed 17920346. Source: UniProtKB

cell proliferation

Inferred from mutant phenotype Ref.11. Source: UniProtKB

inner cell mass cell proliferation

Inferred from electronic annotation. Source: Ensembl

leukocyte chemotaxis

Inferred from direct assay PubMed 14743349. Source: UniProtKB

mature ribosome assembly

Inferred from direct assay Ref.16. Source: UniProtKB

mitotic spindle stabilization

Inferred from direct assay PubMed 18324336. Source: UniProtKB

rRNA processing

Inferred from mutant phenotype Ref.9. Source: UniProtKB

ribosomal large subunit biogenesis

Inferred from Biological aspect of Ancestor. Source: RefGenome

   Cellular_componentcytoplasm

Inferred from direct assay Ref.7PubMed 18324336. Source: UniProtKB

nucleolus

Inferred from direct assay Ref.7Ref.8. Source: UniProtKB

nucleoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from direct assay Ref.7PubMed 18324336. Source: UniProtKB

spindle pole

Inferred from direct assay PubMed 18324336Ref.11. Source: UniProtKB

   Molecular_functionmicrotubule binding

Inferred from direct assay PubMed 18324336. Source: UniProtKB

poly(A) RNA binding

Inferred from direct assay PubMed 22658674. Source: UniProtKB

rRNA binding

Inferred from direct assay Ref.8. Source: UniProtKB

ribosome binding

Inferred from direct assay Ref.16. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.6
Chain2 – 250249Ribosome maturation protein SBDS
PRO_0000123762

Amino acid modifications

Modified residue21N-acetylserine Ref.6 Ref.13 Ref.14

Natural variations

Natural variant81N → K in SDS. Ref.1
Corresponds to variant rs28942099 [ dbSNP | Ensembl ].
VAR_015390
Natural variant441E → G in SDS. Ref.1
VAR_015391
Natural variant671K → E in SDS. Ref.1
VAR_015392
Natural variant871I → S in SDS. Ref.1
VAR_015393
Natural variant1261R → T in SDS; strongly reduced release of EIF6 from pre-60S ribosome subunits. Ref.1 Ref.16
VAR_015394
Natural variant1691R → C in SDS. Ref.1
VAR_015395
Natural variant2121I → T in SDS. Ref.1
Corresponds to variant rs79344818 [ dbSNP | Ensembl ].
VAR_015396

Experimental info

Mutagenesis1511K → N: Strongly reduced release of EIF6 from pre-60S ribosome subunits. Ref.16
Sequence conflict41 – 433SGV → RAW in AAD34092. Ref.2
Sequence conflict891T → A in AAD34092. Ref.2
Sequence conflict1051E → G in AAD34092. Ref.2
Sequence conflict1141I → F in AAD34092. Ref.2
Sequence conflict1261R → G in AAD34092. Ref.2
Sequence conflict1431S → L in AAD34092. Ref.2
Sequence conflict1461T → P in AAD34092. Ref.2

Secondary structure

.................................................. 250
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9Y3A5 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: D35C43003C05F5A7

FASTA25028,764
        10         20         30         40         50         60 
MSIFTPTNQI RLTNVAVVRM KRAGKRFEIA CYKNKVVGWR SGVEKDLDEV LQTHSVFVNV 

        70         80         90        100        110        120 
SKGQVAKKED LISAFGTDDQ TEICKQILTK GEVQVSDKER HTQLEQMFRD IATIVADKCV 

       130        140        150        160        170        180 
NPETKRPYTV ILIERAMKDI HYSVKTNKST KQQALEVIKQ LKEKMKIERA HMRLRFILPV 

       190        200        210        220        230        240 
NEGKKLKEKL KPLIKVIESE DYGQQLEIVC LIDPGCFREI DELIKKETKG KGSLEVLNLK 

       250 
DVEEGDEKFE 

« Hide

References

« Hide 'large scale' references
[1]"Mutations in SBDS are associated with Shwachman-Diamond syndrome."
Boocock G.R.B., Morrison J.A., Popovic M., Richards N., Ellis L., Durie P.R., Rommens J.M.
Nat. Genet. 33:97-101(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANTS SDS LYS-8; GLY-44; GLU-67; SER-87; THR-126; CYS-169 AND THR-212.
[2]"Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics."
Lai C.-H., Chou C.-Y., Ch'ang L.-Y., Liu C.-S., Lin W.-C.
Genome Res. 10:703-713(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Brain cortex and Ovarian carcinoma.
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: PNS.
[6]Bienvenut W.V., Claeys D.
Submitted (NOV-2005) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 2-19, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY.
Tissue: Platelet.
[7]"The Shwachman-Diamond SBDS protein localizes to the nucleolus."
Austin K.M., Leary R.J., Shimamura A.
Blood 106:1253-1258(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[8]"The human Shwachman-Diamond syndrome protein, SBDS, associates with ribosomal RNA."
Ganapathi K.A., Austin K.M., Lee C.S., Dias A., Malsch M.M., Reed R., Shimamura A.
Blood 110:1458-1465(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH NPM1 AND THE 60S RIBOSOMAL SUBUNIT, SUBCELLULAR LOCATION.
[9]"The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels."
Hesling C., Oliveira C.C., Castilho B.A., Zanchin N.I.
Exp. Cell Res. 313:4180-4195(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH NIP7.
[10]"Shwachman-Bodian Diamond syndrome is a multi-functional protein implicated in cellular stress responses."
Ball H.L., Zhang B., Riches J.J., Gandhi R., Li J., Rommens J.M., Myers J.S.
Hum. Mol. Genet. 18:3684-3695(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH RPA1; PRKDC AND THE 60S RIBOSOME SUBUNIT.
[11]"SBDS expression and localization at the mitotic spindle in human myeloid progenitors."
Orelio C., Verkuijlen P., Geissler J., van den Berg T.K., Kuijpers T.W.
PLoS ONE 4:E7084-E7084(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[12]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]"Structure, dynamics, and RNA interaction analysis of the human SBDS protein."
de Oliveira J.F., Sforca M.L., Blumenschein T.M., Goldfeder M.B., Guimaraes B.G., Oliveira C.C., Zanchin N.I., Zeri A.C.
J. Mol. Biol. 396:1053-1069(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR, RNA-BINDING.
[16]"Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome."
Finch A.J., Hilcenko C., Basse N., Drynan L.F., Goyenechea B., Menne T.F., Gonzalez Fernandez A., Simpson P., D'Santos C.S., Arends M.J., Donadieu J., Bellanne-Chantelot C., Costanzo M., Boone C., McKenzie A.N., Freund S.M., Warren A.J.
Genes Dev. 25:917-929(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR, FUNCTION, CHARACTERIZATION OF VARIANT SDS THR-126, MUTAGENESIS OF LYS-151.
+Additional computationally mapped references.

Web resources

SBDSbase

SBDS mutation db

GeneReviews

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_057122.2. NM_016038.2.
UniGeneHs.110445.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2KDONMR-A1-250[»]
2L9NNMR-A1-250[»]
ProteinModelPortalQ9Y3A5.
SMRQ9Y3A5. Positions 1-250.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid119307. 35 interactions.
IntActQ9Y3A5. 1 interaction.
MINTMINT-3085538.
STRING9606.ENSP00000246868.

PTM databases

PhosphoSiteQ9Y3A5.

Polymorphism databases

DMDM28380824.

Proteomic databases

PaxDbQ9Y3A5.
PeptideAtlasQ9Y3A5.
PRIDEQ9Y3A5.

Protocols and materials databases

DNASU51119.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000246868; ENSP00000246868; ENSG00000126524.
GeneID51119.
KEGGhsa:51119.
UCSCuc003tvm.1. human.

Organism-specific databases

CTD51119.
GeneCardsGC07M066452.
HGNCHGNC:19440. SBDS.
HPAHPA028891.
MIM260400. phenotype.
607444. gene.
neXtProtNX_Q9Y3A5.
Orphanet88. Idiopathic aplastic anemia.
811. Shwachman-Diamond syndrome.
PharmGKBPA134978742.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1500.
HOGENOMHOG000216685.
HOVERGENHBG039762.
InParanoidQ9Y3A5.
KOK14574.
OMARSGIETD.
OrthoDBEOG7XWPPD.
PhylomeDBQ9Y3A5.
TreeFamTF300881.

Gene expression databases

ArrayExpressQ9Y3A5.
BgeeQ9Y3A5.
CleanExHS_SBDS.
GenevestigatorQ9Y3A5.

Family and domain databases

Gene3D3.30.1250.10. 1 hit.
InterProIPR018978. Ribosome_mat_SBDS_C.
IPR018023. Ribosome_mat_SBDS_CS.
IPR019783. Ribosome_mat_SBDS_N.
IPR002140. Ribosome_maturation_pr_SBDS.
[Graphical view]
PANTHERPTHR10927. PTHR10927. 1 hit.
PfamPF01172. SBDS. 1 hit.
PF09377. SBDS_C. 1 hit.
[Graphical view]
SUPFAMSSF89895. SSF89895. 1 hit.
TIGRFAMsTIGR00291. RNA_SBDS. 1 hit.
PROSITEPS01267. UPF0023. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSBDS. human.
EvolutionaryTraceQ9Y3A5.
GeneWikiSBDS.
GenomeRNAi51119.
NextBio53897.
PROQ9Y3A5.
SOURCESearch...

Entry information

Entry nameSBDS_HUMAN
AccessionPrimary (citable) accession number: Q9Y3A5
Secondary accession number(s): A8K0P4, Q96FX0, Q9NV53
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 127 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 7

Human chromosome 7: entries, gene names and cross-references to MIM