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16  structures 930  species 0  interactions 1051  sequences 39  architectures

Family: EFTUD2 (PF16004)

Summary: 116 kDa U5 small nuclear ribonucleoprotein component N-terminus

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This is the Wikipedia entry entitled "EFTUD2". More...

EFTUD2 Edit Wikipedia article

EFTUD2
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases EFTUD2, MFDGA, MFDM, SNRNP116, Snrp116, Snu114, U5-116KD, elongation factor Tu GTP binding domain containing 2
External IDs MGI: 1336880 HomoloGene: 3133 GeneCards: EFTUD2
Gene location (Human)
Chromosome 17 (human)
Chr. Chromosome 17 (human)[1]
Chromosome 17 (human)
Genomic location for EFTUD2
Genomic location for EFTUD2
Band n/a Start 44,849,943 bp[1]
End 44,899,662 bp[1]
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001142605
NM_001258353
NM_001258354
NM_004247

NM_001109995
NM_011431

RefSeq (protein)

NP_001136077
NP_001245282
NP_001245283
NP_004238

NP_001103465
NP_035561

Location (UCSC) Chr 17: 44.85 – 44.9 Mb Chr 17: 102.84 – 102.88 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

116 kDa U5 small nuclear ribonucleoprotein component is a protein that in humans is encoded by the EFTUD2 gene.[5][6]

Disease associations

Heterozygous loss-of-function mutations in EFTUD2 cause Mandibulofacial Dysostosis with Microcephaly (MFDM; OMIM #610536),[7] a multiple malformation syndrome comprising progressive microcephaly (present in all affected individuals), craniofacial skeletal anomalies, cleft palate, deafness, choanal atresia, small stature, and/or cardiac and thumb anomalies.

Interactions

EFTUD2 has been shown to interact with WDR57[8][9] and PRPF8.[9]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000108883 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000020929 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ Fabrizio P, Laggerbauer B, Lauber J, Lane WS, Lührmann R (Jul 1997). "An evolutionarily conserved U5 snRNP-specific protein is a GTP-binding factor closely related to the ribosomal translocase EF-2". The EMBO Journal. 16 (13): 4092–106. PMC 1170032Freely accessible. PMID 9233818. doi:10.1093/emboj/16.13.4092. 
  6. ^ "Entrez Gene: EFTUD2 elongation factor Tu GTP binding domain containing 2". 
  7. ^ Lines MA, Huang L, Schwartzentruber J, Douglas SL, Lynch DC, Beaulieu C, Guion-Almeida ML, Zechi-Ceide RM, Gener B, Gillessen-Kaesbach G, Nava C, Baujat G, Horn D, Kini U, Caliebe A, Alanay Y, Utine GE, Lev D, Kohlhase J, Grix AW, Lohmann DR, Hehr U, Böhm D, Majewski J, Bulman DE, Wieczorek D, Boycott KM (Feb 2012). "Haploinsufficiency of a spliceosomal GTPase encoded by EFTUD2 causes mandibulofacial dysostosis with microcephaly". American Journal of Human Genetics. 90 (2): 369–77. PMC 3276671Freely accessible. PMID 22305528. doi:10.1016/j.ajhg.2011.12.023. 
  8. ^ Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D (2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. PMC 1847948Freely accessible. PMID 17353931. doi:10.1038/msb4100134. 
  9. ^ a b Achsel T, Ahrens K, Brahms H, Teigelkamp S, Lührmann R (Nov 1998). "The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein". Molecular and Cellular Biology. 18 (11): 6756–66. PMC 109259Freely accessible. PMID 9774689. doi:10.1128/mcb.18.11.6756. 

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.

116 kDa U5 small nuclear ribonucleoprotein component N-terminus Provide feedback

No Pfam abstract.

Literature references

  1. Fabrizio P, Laggerbauer B, Lauber J, Lane WS, Luhrmann R;, EMBO J. 1997;16:4092-4106.: An evolutionarily conserved U5 snRNP-specific protein is a GTP-binding factor closely related to the ribosomal translocase EF-2. PUBMED:9233818 EPMC:9233818


This tab holds annotation information from the InterPro database.

InterPro entry IPR031950

This entry represents the N-terminal domain of U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116kDa). It is also found in Snu114p, a 114 kDa protein homologous to U5-116kDa that has been identified in Saccharomyces cerevisiae [PUBMED:9233818]. Both proteins seem to have a role in pre-mRNA splicing process.

Domain organisation

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Alignments

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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  Seed
(148)
Full
(1051)
Representative proteomes UniProt
(1479)
NCBI
(1633)
Meta
(3)
RP15
(311)
RP35
(604)
RP55
(846)
RP75
(1034)
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Key: ✓ available, x not generated, not available.

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  Seed
(148)
Full
(1051)
Representative proteomes UniProt
(1479)
NCBI
(1633)
Meta
(3)
RP15
(311)
RP35
(604)
RP55
(846)
RP75
(1034)
Alignment:
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  Seed
(148)
Full
(1051)
Representative proteomes UniProt
(1479)
NCBI
(1633)
Meta
(3)
RP15
(311)
RP35
(604)
RP55
(846)
RP75
(1034)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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...

Trees

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.

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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

Seed source: Jackhmmer:Q8IMM5
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R
Number in seed: 148
Number in full: 1051
Average length of the domain: 111.00 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 11.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 32.2 32.2
Trusted cut-off 32.3 32.2
Noise cut-off 32.1 31.8
Model length: 122
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Structures

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 EFTUD2 domain has been found. There are 16 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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