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Protein

Protein SEC13 homolog

Gene

SEC13

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 CASTOR1 (PubMed:25457612, PubMed:27487210).3 Publications

GO - Molecular functioni

  • identical protein binding Source: IntAct
  • structural molecule activity Source: InterPro

GO - Biological processi

Keywordsi

Biological processER-Golgi transport, mRNA transport, Protein transport, Translocation, Transport

Enzyme and pathway databases

ReactomeiR-HSA-141444 Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
R-HSA-204005 COPII-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
SIGNORiP55735

Protein family/group databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Protein SEC13 homologCurated
Alternative name(s):
GATOR complex protein SEC13Curated
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

EuPathDBiHostDB:ENSG00000157020.17
HGNCiHGNC:10697 SEC13
MIMi600152 gene
neXtProtiNX_P55735

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

Cytoplasmic vesicle, Endoplasmic reticulum, Lysosome, 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
ProteomicsDBi56858

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 CASTOR2 and CASTOR1; 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

Show more details

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi112296, 83 interactors
CORUMiP55735
DIPiDIP-39091N
IntActiP55735, 59 interactors
MINTiP55735
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

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
InterProiView protein in InterPro
IPR037596 Sec13
IPR037363 Sec13/Seh1_fam
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
PANTHERiPTHR11024 PTHR11024, 1 hit
PTHR11024:SF2 PTHR11024:SF2, 1 hit
PfamiView protein in Pfam
PF00400 WD40, 5 hits
SMARTiView protein in SMART
SM00320 WD40, 6 hits
SUPFAMiSSF50978 SSF50978, 1 hit
PROSITEiView protein in PROSITE
PS50082 WD_REPEATS_2, 3 hits
PS50294 WD_REPEATS_REGION, 1 hit

Sequences (4)i

Sequence statusi: Complete.

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

This entry describes 4 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
Isoform 4 (identifier: P55735-4) [UniParc]FASTAAdd to basket

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

Note: No experimental confirmation available.
Show »
Length:325
Mass (Da):35,857
Checksum:iFF2931B0935BA1FB
GO

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 dbSNP:rs34078590Ensembl.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
Alternative sequenceiVSP_0589661M → MGKM in isoform 4. 1

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
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 [P55735-4]
NP_899195.1, NM_183352.2 [P55735-1]
XP_005265436.1, XM_005265379.2 [P55735-4]
XP_016862508.1, XM_017007019.1 [P55735-3]
UniGeneiHs.166924
Hs.672979

Genome annotation databases

EnsembliENST00000337354; ENSP00000336566; ENSG00000157020 [P55735-4]
ENST00000350697; 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

Similar proteinsi

Entry informationi

Entry nameiSEC13_HUMAN
AccessioniPrimary (citable) accession number: P55735
Secondary accession number(s): A8MV37
, B4DXJ1, Q5BJF0, Q9BRM6, Q9BUG7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2007
Last modified: June 20, 2018
This is version 180 of the entry and version 3 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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