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Protein

Protein transport protein SEC13

Gene

SEC13

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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. It is one of 5 proteins constituting the COPII coat, which is involved in anterograde (ER to Golgi) double-membrane transport vesicle formation. First the small GTPase SAR1, activated by and binding to the integral ER membrane protein SEC12, exchanges GDP for GTP and recruits the heterodimer SEC23/24, which in turn recruits the heterotetramer SEC13-SEC31. The polymerization of COPII coat complexes then causes physically the deformation (budding) of the membrane, leading to the creation of a transport vesicle. The COPII complex is dissociated upon SAR1-GTP hydrolysis to SAR1-GDP. SEC23 functions as the SAR1 GTPase activating protein, whose activity is stimulated in the presence of SEC13/31. SEC13 is directly or indirectly required for normal ER membrane and nuclear envelope morphology. It also functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. SEC13 is required for efficient mRNA export from the nucleus to the cytoplasm and for correct nuclear pore biogenesis and distribution. Component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis.19 Publications

GO - Molecular functioni

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

GO - Biological processi

  • COPII-coated vesicle budding Source: SGD
  • ER-associated ubiquitin-dependent protein catabolic process Source: SGD
  • mRNA transport Source: UniProtKB-KW
  • nuclear pore distribution Source: SGD
  • positive regulation of GTPase activity Source: SGD
  • positive regulation of TORC1 signaling Source: SGD
  • positive regulation of transcription, DNA-templated Source: SGD
  • protein transport Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

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

Enzyme and pathway databases

BioCyciYEAST:G3O-32326-MONOMER.
ReactomeiR-SCE-204005. COPII (Coat Protein 2) Mediated Vesicle Transport.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein transport protein SEC13
Gene namesi
Name:SEC13
Synonyms:ANU3
Ordered Locus Names:YLR208W
ORF Names:L8167.4
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR208W.
SGDiS000004198. SEC13.

Subcellular locationi

GO - Cellular componenti

  • COPII vesicle coat Source: SGD
  • endoplasmic reticulum membrane Source: UniProtKB-SubCell
  • Golgi membrane Source: GOC
  • nuclear pore outer ring Source: SGD
  • Seh1-associated complex Source: SGD
  • vacuolar membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi176 – 1761G → R: Leads to mislocalization of NPCs and overproliferation of the nuclear and ER membranes at 34 degree Celsius. 1 Publication
Mutagenesisi224 – 2241S → K: Growth inhibited above 30 degrees Celsius. 1 Publication
Mutagenesisi262 – 2621W → R: Growth inhibited above 30 degrees Celsius. 1 Publication
Mutagenesisi266 – 2661G → D: Growth inhibited above 34 degrees Celsius. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 297297Protein transport protein SEC13PRO_0000051206Add
BLAST

Proteomic databases

MaxQBiQ04491.

Interactioni

Subunit structurei

The basic repeat unit of a COPII coated vesicle is composed of 5 proteins: the small GTPase SAR1, the heterodimeric SEC23-SEC24 complex, and the heterotetrameric SEC13-SEC31 complex. This repeat unit polymerizes to induce membrane deformation into a transport vesicle. The nuclear pore complex (NPC) constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the passive diffusion of ions and small molecules and the active, nuclear transport receptor-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal subunits across the nuclear envelope. The 55-60 MDa NPC is composed of at least 31 different subunits: ASM4, CDC31, GLE1, GLE2, NDC1, NIC96, NSP1, NUP1, NUP2, NUP100, NUP116, NUP120, NUP133, NUP145, NUP157, NUP159, NUP170, NUP188, NUP192, NUP42, NUP49, NUP53, NUP57, NUP60, NUP82, NUP84, NUP85, POM152, POM34, SEH1 and SEC1. Due to its 8-fold rotational symmetry, all subunits are present with 8 copies or multiples thereof. SEC13 is part of the heptameric 0.5 MDa autoassembling NUP84 NPC subcomplex (NUP84, NUP85, NUP120, NUP133, NUP145C, SEC13 and SEH1). Component of the SEA complex composed of at least IML1/SEA1, RTC1/SEA2, MTC5/SEA3, NPR2, NPR3, SEA4, SEC13 and SEH1.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself2EBI-16529,EBI-16529
MTC5Q038975EBI-16529,EBI-32422
NUP145P496878EBI-16529,EBI-11730
SEC31P389688EBI-16529,EBI-20524

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi31476. 150 interactions.
DIPiDIP-1826N.
IntActiQ04491. 26 interactions.
MINTiMINT-402427.

Structurei

Secondary structure

1
297
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 43Combined sources
Beta strandi5 – 73Combined sources
Beta strandi12 – 176Combined sources
Beta strandi21 – 288Combined sources
Beta strandi33 – 386Combined sources
Beta strandi47 – 493Combined sources
Beta strandi56 – 616Combined sources
Helixi64 – 663Combined sources
Beta strandi68 – 747Combined sources
Beta strandi79 – 879Combined sources
Beta strandi93 – 953Combined sources
Beta strandi98 – 1003Combined sources
Beta strandi102 – 1076Combined sources
Helixi110 – 1123Combined sources
Beta strandi114 – 1207Combined sources
Beta strandi123 – 1308Combined sources
Beta strandi132 – 1343Combined sources
Beta strandi139 – 1424Combined sources
Beta strandi148 – 1536Combined sources
Beta strandi157 – 1615Combined sources
Turni162 – 1654Combined sources
Beta strandi166 – 1705Combined sources
Beta strandi172 – 1776Combined sources
Beta strandi182 – 1887Combined sources
Turni189 – 1924Combined sources
Beta strandi193 – 2008Combined sources
Beta strandi207 – 2126Combined sources
Beta strandi217 – 22610Combined sources
Beta strandi227 – 2293Combined sources
Beta strandi231 – 2388Combined sources
Beta strandi244 – 2518Combined sources
Beta strandi257 – 2626Combined sources
Beta strandi264 – 2663Combined sources
Beta strandi269 – 2735Combined sources
Beta strandi274 – 2763Combined sources
Beta strandi278 – 2836Combined sources
Beta strandi285 – 2873Combined sources
Beta strandi289 – 2913Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PM6X-ray2.45B/D1-297[»]
2PM7X-ray2.35B/D1-297[»]
2PM9X-ray3.30B1-297[»]
3IKOX-ray3.20A/D/G1-297[»]
3JROX-ray4.00A1-297[»]
3JRPX-ray2.60A1-297[»]
3MZKX-ray2.69A/D1-297[»]
3MZLX-ray2.80A/C/E/G1-297[»]
4BZJelectron microscopy40.00B/F2-292[»]
4BZKelectron microscopy40.00B/F1-292[»]
4XMMX-ray7.38A1-297[»]
4XMNX-ray7.60A1-297[»]
ProteinModelPortaliQ04491.
SMRiQ04491. Positions 1-297.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ04491.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati7 – 4640WD 1Add
BLAST
Repeati51 – 9242WD 2Add
BLAST
Repeati97 – 13842WD 3Add
BLAST
Repeati143 – 19553WD 4Add
BLAST
Repeati202 – 24443WD 5Add
BLAST
Repeati252 – 29140WD 6Add
BLAST

Sequence similaritiesi

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

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

GeneTreeiENSGT00550000075049.
HOGENOMiHOG000216895.
InParanoidiQ04491.
KOiK14004.
OMAiVWEFVNG.
OrthoDBiEOG092C3FZO.

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. 2 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]

Sequencei

Sequence statusi: Complete.

Q04491-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVVIANAHNE LIHDAVLDYY GKRLATCSSD KTIKIFEVEG ETHKLIDTLT
60 70 80 90 100
GHEGPVWRVD WAHPKFGTIL ASCSYDGKVL IWKEENGRWS QIAVHAVHSA
110 120 130 140 150
SVNSVQWAPH EYGPLLLVAS SDGKVSVVEF KENGTTSPII IDAHAIGVNS
160 170 180 190 200
ASWAPATIEE DGEHNGTKES RKFVTGGADN LVKIWKYNSD AQTYVLESTL
210 220 230 240 250
EGHSDWVRDV AWSPTVLLRS YLASVSQDRT CIIWTQDNEQ GPWKKTLLKE
260 270 280 290
EKFPDVLWRA SWSLSGNVLA LSGGDNKVTL WKENLEGKWE PAGEVHQ
Length:297
Mass (Da):33,043
Last modified:October 1, 1993 - v1
Checksum:iA94388B4B9CB77FE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L05929 Genomic DNA. Translation: AAA35028.1.
U14913 Genomic DNA. Translation: AAB67426.1.
BK006945 Genomic DNA. Translation: DAA09525.1.
PIRiA45442.
RefSeqiNP_013309.1. NM_001182095.1.

Genome annotation databases

EnsemblFungiiYLR208W; YLR208W; YLR208W.
GeneIDi850905.
KEGGisce:YLR208W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L05929 Genomic DNA. Translation: AAA35028.1.
U14913 Genomic DNA. Translation: AAB67426.1.
BK006945 Genomic DNA. Translation: DAA09525.1.
PIRiA45442.
RefSeqiNP_013309.1. NM_001182095.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PM6X-ray2.45B/D1-297[»]
2PM7X-ray2.35B/D1-297[»]
2PM9X-ray3.30B1-297[»]
3IKOX-ray3.20A/D/G1-297[»]
3JROX-ray4.00A1-297[»]
3JRPX-ray2.60A1-297[»]
3MZKX-ray2.69A/D1-297[»]
3MZLX-ray2.80A/C/E/G1-297[»]
4BZJelectron microscopy40.00B/F2-292[»]
4BZKelectron microscopy40.00B/F1-292[»]
4XMMX-ray7.38A1-297[»]
4XMNX-ray7.60A1-297[»]
ProteinModelPortaliQ04491.
SMRiQ04491. Positions 1-297.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31476. 150 interactions.
DIPiDIP-1826N.
IntActiQ04491. 26 interactions.
MINTiMINT-402427.

Proteomic databases

MaxQBiQ04491.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR208W; YLR208W; YLR208W.
GeneIDi850905.
KEGGisce:YLR208W.

Organism-specific databases

EuPathDBiFungiDB:YLR208W.
SGDiS000004198. SEC13.

Phylogenomic databases

GeneTreeiENSGT00550000075049.
HOGENOMiHOG000216895.
InParanoidiQ04491.
KOiK14004.
OMAiVWEFVNG.
OrthoDBiEOG092C3FZO.

Enzyme and pathway databases

BioCyciYEAST:G3O-32326-MONOMER.
ReactomeiR-SCE-204005. COPII (Coat Protein 2) Mediated Vesicle Transport.

Miscellaneous databases

EvolutionaryTraceiQ04491.
PROiQ04491.

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. 2 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_YEAST
AccessioniPrimary (citable) accession number: Q04491
Secondary accession number(s): D6VYK9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: September 7, 2016
This is version 159 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 21400 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

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.