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Protein

Protein SEC13 homolog

Gene

SEC13

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Functions as a component of the nuclear pore complex (NPC) and the COPII coat. At the endoplasmic reticulum, SEC13 is involved in the biogenesis of COPII-coated vesicles.1 Publication
As a component of the GATOR subcomplex GATOR2, functions within the amino acid-sensing branch of the TORC1 signaling pathway. Indirectly activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex (PubMed:23723238). It is negatively regulated by the upstream amino acid sensors SESN2 and GATSL3 (PubMed:25457612, PubMed:27487210).3 Publications

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

ER-Golgi transport, mRNA transport, Protein transport, Translocation, Transport

Enzyme and pathway databases

BioCyciZFISH:ENSG00000157020-MONOMER.
ReactomeiR-HSA-204005. COPII (Coat Protein 2) Mediated Vesicle Transport.
R-HSA-2132295. MHC class II antigen presentation.
R-HSA-2467813. Separation of Sister Chromatids.
R-HSA-2500257. Resolution of Sister Chromatid Cohesion.
R-HSA-5663220. RHO GTPases Activate Formins.
R-HSA-68877. Mitotic Prometaphase.
R-HSA-983170. Antigen Presentation: Folding, assembly and peptide loading of class I MHC.
SignaLinkiP55735.

Protein family/group databases

TCDBi1.I.1.1.3. the nuclear pore complex (npc) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein SEC13 homolog
Alternative name(s):
SEC13-like protein 1
SEC13-related protein
Gene namesi
Name:SEC13
Synonyms:D3S1231E, SEC13L1, SEC13R
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:10697. SEC13.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • endoplasmic reticulum membrane Source: Reactome
  • ER to Golgi transport vesicle membrane Source: Reactome
  • extracellular exosome Source: UniProtKB
  • GATOR2 complex Source: SGD
  • Golgi membrane Source: GOC
  • intracellular membrane-bounded organelle Source: HPA
  • nuclear envelope Source: UniProtKB
  • nuclear pore outer ring Source: UniProtKB
  • nucleoplasm Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasmic vesicle, Endoplasmic reticulum, Membrane, Nuclear pore complex, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi6396.
OpenTargetsiENSG00000157020.
PharmGKBiPA35620.

Polymorphism and mutation databases

DMDMi50403748.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources2 Publications
ChainiPRO_00000512032 – 322Protein SEC13 homologAdd BLAST321

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylvalineCombined sources1 Publication1
Modified residuei184PhosphoserineCombined sources1
Modified residuei309PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiP55735.
MaxQBiP55735.
PaxDbiP55735.
PeptideAtlasiP55735.
PRIDEiP55735.

PTM databases

iPTMnetiP55735.
PhosphoSitePlusiP55735.
SwissPalmiP55735.

Expressioni

Gene expression databases

BgeeiENSG00000157020.
CleanExiHS_SEC13.
ExpressionAtlasiP55735. baseline and differential.
GenevisibleiP55735. HS.

Organism-specific databases

HPAiHPA035292.
HPA057943.

Interactioni

Subunit structurei

At the nuclear pore: component of the Y-shaped Nup107-160 subcomplex of the nuclear pore complex (NPC). The Nup107-160 subcomplex includes NUP160, NUP133, NUP107, NUP98, NUP85, NUP43, NUP37, SEH1 and SEC13. At the COPII coat complex: interacts with SEC31A and SEC31B. Within the GATOR complex, component of the GATOR2 subcomplex, made of MIOS, SEC13, SEH1L, WDR24 and WDR59. The GATOR complex strongly interacts with RRAGA/RRAGC and RRAGB/RRAGC heterodimers (PubMed:14517296, PubMed:16495487, PubMed:16957052, PubMed:18160040, PubMed:23723238). The GATOR2 complex interacts with GATSL2 and GATSL3; the interaction is negatively regulated by arginine (PubMed:26972053). The GATOR2 complex interacts with SESN1, SESN2 and SESN3; the interaction is negatively regulated by amino acids (PubMed:25263562, PubMed:25457612).8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-1046596,EBI-1046596
NUP145P4968715EBI-1046596,EBI-11730From a different organism.
SEC16BQ96JE7-25EBI-1046596,EBI-10215083
SEH1LQ96EE33EBI-1046596,EBI-922818
TRAF5O004633EBI-1046596,EBI-523498

Protein-protein interaction databases

BioGridi112296. 79 interactors.
DIPiDIP-39091N.
IntActiP55735. 45 interactors.
MINTiMINT-1154053.
STRINGi9606.ENSP00000312122.

Structurei

Secondary structure

1322
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi16 – 21Combined sources6
Helixi23 – 25Combined sources3
Beta strandi27 – 32Combined sources6
Beta strandi35 – 43Combined sources9
Beta strandi46 – 54Combined sources9
Beta strandi60 – 65Combined sources6
Helixi68 – 70Combined sources3
Beta strandi74 – 78Combined sources5
Beta strandi83 – 86Combined sources4
Beta strandi89 – 91Combined sources3
Beta strandi95 – 99Combined sources5
Beta strandi108 – 111Combined sources4
Turni114 – 116Combined sources3
Beta strandi120 – 123Combined sources4
Beta strandi125 – 127Combined sources3
Beta strandi129 – 134Combined sources6
Beta strandi136 – 138Combined sources3
Beta strandi140 – 142Combined sources3
Beta strandi148 – 151Combined sources4
Beta strandi181 – 183Combined sources3
Beta strandi193 – 196Combined sources4
Beta strandi202 – 206Combined sources5
Beta strandi215 – 219Combined sources5
Beta strandi230 – 235Combined sources6
Beta strandi239 – 244Combined sources6
Beta strandi246 – 249Combined sources4
Beta strandi257 – 260Combined sources4
Beta strandi265 – 270Combined sources6
Turni272 – 274Combined sources3
Beta strandi277 – 284Combined sources8
Beta strandi286 – 291Combined sources6
Beta strandi297 – 302Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BG0X-ray3.15A/D/E/H1-316[»]
3BG1X-ray3.00A/D/E/H1-316[»]
5A9Qelectron microscopy23.006/F/O/X1-322[»]
ProteinModelPortaliP55735.
SMRiP55735.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP55735.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati11 – 50WD 1Add BLAST40
Repeati55 – 96WD 2Add BLAST42
Repeati101 – 144WD 3Add BLAST44
Repeati148 – 204WD 4Add BLAST57
Repeati210 – 253WD 5Add BLAST44
Repeati260 – 299WD 6Add BLAST40

Sequence similaritiesi

Belongs to the WD repeat SEC13 family.Curated
Contains 6 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG1332. Eukaryota.
ENOG410XPFM. LUCA.
GeneTreeiENSGT00550000075049.
HOGENOMiHOG000216895.
HOVERGENiHBG057343.
InParanoidiP55735.
KOiK14004.
OMAiREDNDRW.
OrthoDBiEOG091G0DTE.
PhylomeDBiP55735.
TreeFamiTF300815.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF00400. WD40. 5 hits.
[Graphical view]
SMARTiSM00320. WD40. 6 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS50082. WD_REPEATS_2. 3 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P55735-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MVSVINTVDT SHEDMIHDAQ MDYYGTRLAT CSSDRSVKIF DVRNGGQILI
60 70 80 90 100
ADLRGHEGPV WQVAWAHPMY GNILASCSYD RKVIIWREEN GTWEKSHEHA
110 120 130 140 150
GHDSSVNSVC WAPHDYGLIL ACGSSDGAIS LLTYTGEGQW EVKKINNAHT
160 170 180 190 200
IGCNAVSWAP AVVPGSLIDH PSGQKPNYIK RFASGGCDNL IKLWKEEEDG
210 220 230 240 250
QWKEEQKLEA HSDWVRDVAW APSIGLPTST IASCSQDGRV FIWTCDDASS
260 270 280 290 300
NTWSPKLLHK FNDVVWHVSW SITANILAVS GGDNKVTLWK ESVDGQWVCI
310 320
SDVNKGQGSV SASVTEGQQN EQ
Length:322
Mass (Da):35,541
Last modified:January 23, 2007 - v3
Checksum:i18E29627D87FB3DD
GO
Isoform 2 (identifier: P55735-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-14: Missing.

Note: No experimental confirmation available.
Show »
Length:308
Mass (Da):34,012
Checksum:iF4D5BC3F757FE7BB
GO
Isoform 3 (identifier: P55735-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MREPVLTWCVPLELLCSHPLPLSAFLKSQVKLYTYRACAGKDEMGKM

Note: No experimental confirmation available.
Show »
Length:368
Mass (Da):40,747
Checksum:iE738D9D307CF2308
GO

Sequence cautioni

The sequence AAH02634 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti51A → V in L09260 (PubMed:7987303).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_053413172S → L.Corresponds to variant rs34078590dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0461911 – 14Missing in isoform 2. 1 PublicationAdd BLAST14
Alternative sequenceiVSP_0546951M → MREPVLTWCVPLELLCSHPL PLSAFLKSQVKLYTYRACAG KDEMGKM in isoform 3. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L09260 mRNA. No translation available.
AF052155 mRNA. No translation available.
AK301999 mRNA. Translation: BAG63403.1.
AC022384 Genomic DNA. No translation available.
BC002634 mRNA. Translation: AAH02634.2. Different initiation.
BC006167 mRNA. Translation: AAH06167.1.
BC091506 mRNA. Translation: AAH91506.1.
CCDSiCCDS2599.1. [P55735-1]
CCDS46751.1. [P55735-2]
CCDS63540.1. [P55735-3]
RefSeqiNP_001129498.1. NM_001136026.2. [P55735-3]
NP_001129704.1. NM_001136232.2. [P55735-2]
NP_109598.2. NM_030673.3.
NP_899195.1. NM_183352.2. [P55735-1]
XP_005265436.1. XM_005265379.2.
XP_016862508.1. XM_017007019.1. [P55735-3]
UniGeneiHs.166924.
Hs.672979.

Genome annotation databases

EnsembliENST00000350697; ENSP00000312122; ENSG00000157020. [P55735-1]
ENST00000383801; ENSP00000373312; ENSG00000157020. [P55735-3]
ENST00000397109; ENSP00000380298; ENSG00000157020. [P55735-2]
GeneIDi6396.
KEGGihsa:6396.
UCSCiuc003bvm.5. human. [P55735-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L09260 mRNA. No translation available.
AF052155 mRNA. No translation available.
AK301999 mRNA. Translation: BAG63403.1.
AC022384 Genomic DNA. No translation available.
BC002634 mRNA. Translation: AAH02634.2. Different initiation.
BC006167 mRNA. Translation: AAH06167.1.
BC091506 mRNA. Translation: AAH91506.1.
CCDSiCCDS2599.1. [P55735-1]
CCDS46751.1. [P55735-2]
CCDS63540.1. [P55735-3]
RefSeqiNP_001129498.1. NM_001136026.2. [P55735-3]
NP_001129704.1. NM_001136232.2. [P55735-2]
NP_109598.2. NM_030673.3.
NP_899195.1. NM_183352.2. [P55735-1]
XP_005265436.1. XM_005265379.2.
XP_016862508.1. XM_017007019.1. [P55735-3]
UniGeneiHs.166924.
Hs.672979.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BG0X-ray3.15A/D/E/H1-316[»]
3BG1X-ray3.00A/D/E/H1-316[»]
5A9Qelectron microscopy23.006/F/O/X1-322[»]
ProteinModelPortaliP55735.
SMRiP55735.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112296. 79 interactors.
DIPiDIP-39091N.
IntActiP55735. 45 interactors.
MINTiMINT-1154053.
STRINGi9606.ENSP00000312122.

Protein family/group databases

TCDBi1.I.1.1.3. the nuclear pore complex (npc) family.

PTM databases

iPTMnetiP55735.
PhosphoSitePlusiP55735.
SwissPalmiP55735.

Polymorphism and mutation databases

DMDMi50403748.

Proteomic databases

EPDiP55735.
MaxQBiP55735.
PaxDbiP55735.
PeptideAtlasiP55735.
PRIDEiP55735.

Protocols and materials databases

DNASUi6396.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000350697; ENSP00000312122; ENSG00000157020. [P55735-1]
ENST00000383801; ENSP00000373312; ENSG00000157020. [P55735-3]
ENST00000397109; ENSP00000380298; ENSG00000157020. [P55735-2]
GeneIDi6396.
KEGGihsa:6396.
UCSCiuc003bvm.5. human. [P55735-1]

Organism-specific databases

CTDi6396.
DisGeNETi6396.
GeneCardsiSEC13.
HGNCiHGNC:10697. SEC13.
HPAiHPA035292.
HPA057943.
MIMi600152. gene.
neXtProtiNX_P55735.
OpenTargetsiENSG00000157020.
PharmGKBiPA35620.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1332. Eukaryota.
ENOG410XPFM. LUCA.
GeneTreeiENSGT00550000075049.
HOGENOMiHOG000216895.
HOVERGENiHBG057343.
InParanoidiP55735.
KOiK14004.
OMAiREDNDRW.
OrthoDBiEOG091G0DTE.
PhylomeDBiP55735.
TreeFamiTF300815.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000157020-MONOMER.
ReactomeiR-HSA-204005. COPII (Coat Protein 2) Mediated Vesicle Transport.
R-HSA-2132295. MHC class II antigen presentation.
R-HSA-2467813. Separation of Sister Chromatids.
R-HSA-2500257. Resolution of Sister Chromatid Cohesion.
R-HSA-5663220. RHO GTPases Activate Formins.
R-HSA-68877. Mitotic Prometaphase.
R-HSA-983170. Antigen Presentation: Folding, assembly and peptide loading of class I MHC.
SignaLinkiP55735.

Miscellaneous databases

ChiTaRSiSEC13. human.
EvolutionaryTraceiP55735.
GeneWikiiSEC13.
GenomeRNAii6396.
PROiP55735.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000157020.
CleanExiHS_SEC13.
ExpressionAtlasiP55735. baseline and differential.
GenevisibleiP55735. HS.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF00400. WD40. 5 hits.
[Graphical view]
SMARTiSM00320. WD40. 6 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS50082. WD_REPEATS_2. 3 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSEC13_HUMAN
AccessioniPrimary (citable) accession number: P55735
Secondary accession number(s): A8MV37
, B4DXJ1, Q5BJF0, Q9BRM6, Q9BUG7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 163 of the entry and version 3 of the sequence. [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

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.