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12  structures 1558  species 0  interactions 1706  sequences 24  architectures

Family: SBDS_C (PF20268)

Summary: SBDS protein, C-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "SBDS". More...

SBDS Edit Wikipedia article

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Available structures
PDBOrtholog search: PDBe RCSB
AliasesSBDS, SDS, SWDS, CGI-97, SBDS ribosome assembly guanine nucleotide exchange factor, ribosome maturation factor, SBDS ribosome maturation factor, SDO1
External IDsOMIM: 607444 MGI: 1913961 HomoloGene: 6438 GeneCards: SBDS
RefSeq (mRNA)



RefSeq (protein)



Location (UCSC)Chr 7: 66.99 – 67 MbChr 5: 130.27 – 130.28 Mb
PubMed search[3][4]
View/Edit HumanView/Edit Mouse

Shwachman-Bodian-Diamond syndrome, also known as SBDS, is a human gene.[5]

Template:PBB Summary


  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000126524 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000025337 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ "Entrez Gene: SBDS Shwachman-Bodian-Diamond syndrome".

Further reading

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

SBDS protein, C-terminal domain Provide feedback

Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants [1] including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. These proteins play a role in RNA metabolism [2,3]. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes [4]. The SBDS protein is composed of three domains. The N-terminal (PF01172) (FYSH) domain (domain I) is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold, the central domain (domain II, PF09377) consists of a three-helical bundle and this C-terminal domain which has a ferredoxin-like fold [3,5].

Literature references

  1. Boocock GR, Morrison JA, Popovic M, Richards N, Ellis L, Durie PR, Rommens JM; , Nat Genet 2003;33:97-101.: Mutations in SBDS are associated with Shwachman-Diamond syndrome. PUBMED:12496757 EPMC:12496757

  2. Savchenko A, Krogan N, Cort JR, Evdokimova E, Lew JM, Yee AA, Sanchez-Pulido L, Andrade MA, Bochkarev A, Watson JD, Kennedy MA, Greenblatt J, Hughes T, Arrowsmith CH, Rommens JM, Edwards AM; , J Biol Chem 2005; [Epub ahead of print]: The SHWACHMAN-Bodian-diamond syndromeprotein family is involved in RNA metabolism. PUBMED:15701634 EPMC:15701634

  3. Shammas C, Menne TF, Hilcenko C, Michell SR, Goyenechea B, Boocock GR, Durie PR, Rommens JM, Warren AJ; , J Biol Chem 2005; [Epub ahead of print]: Structural and mutational analysis of the SBDS protein family: insight into the leukemia-associated shwachman-diamond syndrome. PUBMED:15701631 EPMC:15701631

  4. Menne TF, Goyenechea B, Sanchez-Puig N, Wong CC, Tonkin LM, Ancliff PJ, Brost RL, Costanzo M, Boone C, Warren AJ; , Nat Genet. 2007;39:486-495.: The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomes in yeast. PUBMED:17353896 EPMC:17353896

  5. Finch AJ, Hilcenko C, Basse N, Drynan LF, Goyenechea B, Menne TF, Gonzalez Fernandez A, Simpson P, D'Santos CS, Arends MJ, Donadieu J, Bellanne-Chantelot C, Costanzo M, Boone C, McKenzie AN, Freund SM, Warren AJ;, Genes Dev. 2011;25:917-929.: Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome. PUBMED:21536732 EPMC:21536732

External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan EF-G_C (CL0437), which has the following description:

This superfamily is characterised by being an alpha-beta 2-Layer Sandwich. It is found in EF2 proteins from both prokaryotes and eukaryotes, as well as in some tetracycline resistance proteins, peptide chain release factors ], and in the C-terminal region of the bacterial hypothetical protein, YigZ.

The clan contains the following 7 members:



We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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Representative proteomes UniProt

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

This family is new in this Pfam release.

Seed source: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Chuguransky S
Number in seed: 139
Number in full: 1706
Average length of the domain: 76.2 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 26.77 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 71
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SBDS_C domain has been found. There are 12 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044V0V6 View 3D Structure Click here
A0A077Z7U3 View 3D Structure Click here
A0A0D2E3N3 View 3D Structure Click here
A0A0K0DUR6 View 3D Structure Click here
A0A0K0JM58 View 3D Structure Click here
A0A0N4UPV9 View 3D Structure Click here
A0A175VXT3 View 3D Structure Click here
A0A1C1CM25 View 3D Structure Click here
A0A3P7EAK0 View 3D Structure Click here
C0NX45 View 3D Structure Click here
C1GXD7 View 3D Structure Click here
F8W5Q9 View 3D Structure Click here
G4VJ59 View 3D Structure Click here
K7M771 View 3D Structure Click here
O14179 View 3D Structure Click here
O26781 View 3D Structure Click here
O29759 View 3D Structure Click here
P70122 View 3D Structure Click here
Q07953 View 3D Structure Click here
Q23202 View 3D Structure Click here
Q3SWZ6 View 3D Structure Click here
Q58011 View 3D Structure Click here
Q5AF99 View 3D Structure Click here
Q5RAZ2 View 3D Structure Click here
Q5RK30 View 3D Structure Click here
Q5ZIY4 View 3D Structure Click here
Q6DIT8 View 3D Structure Click here
Q6ZD69 View 3D Structure Click here
Q86KZ5 View 3D Structure Click here
Q9MAR2 View 3D Structure Click here
Q9VRY5 View 3D Structure Click here
Q9Y3A5 View 3D Structure Click here
Q9YCU5 View 3D Structure Click here
U7Q0S6 View 3D Structure Click here