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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

  • 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)DescriptionActionsGraphical viewLength
Mutagenesisi176G → R: Leads to mislocalization of NPCs and overproliferation of the nuclear and ER membranes at 34 degree Celsius. 1 Publication1
Mutagenesisi224S → K: Growth inhibited above 30 degrees Celsius. 1 Publication1
Mutagenesisi262W → R: Growth inhibited above 30 degrees Celsius. 1 Publication1
Mutagenesisi266G → D: Growth inhibited above 34 degrees Celsius. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000512061 – 297Protein transport protein SEC13Add BLAST297

Proteomic databases

MaxQBiQ04491.
PRIDEiQ04491.

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
NUP145P4968712EBI-16529,EBI-11730
SEC31P389688EBI-16529,EBI-20524

Protein-protein interaction databases

BioGridi31476. 151 interactors.
DIPiDIP-1826N.
IntActiQ04491. 26 interactors.
MINTiMINT-402427.

Structurei

Secondary structure

1297
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 4Combined sources3
Beta strandi5 – 7Combined sources3
Beta strandi12 – 17Combined sources6
Beta strandi21 – 28Combined sources8
Beta strandi33 – 38Combined sources6
Beta strandi47 – 49Combined sources3
Beta strandi56 – 61Combined sources6
Helixi64 – 66Combined sources3
Beta strandi68 – 74Combined sources7
Beta strandi79 – 87Combined sources9
Beta strandi93 – 95Combined sources3
Beta strandi98 – 100Combined sources3
Beta strandi102 – 107Combined sources6
Helixi110 – 112Combined sources3
Beta strandi114 – 120Combined sources7
Beta strandi123 – 130Combined sources8
Beta strandi132 – 134Combined sources3
Beta strandi139 – 142Combined sources4
Beta strandi148 – 153Combined sources6
Beta strandi157 – 161Combined sources5
Turni162 – 165Combined sources4
Beta strandi166 – 170Combined sources5
Beta strandi172 – 177Combined sources6
Beta strandi182 – 188Combined sources7
Turni189 – 192Combined sources4
Beta strandi193 – 200Combined sources8
Beta strandi207 – 212Combined sources6
Beta strandi217 – 226Combined sources10
Beta strandi227 – 229Combined sources3
Beta strandi231 – 238Combined sources8
Beta strandi244 – 251Combined sources8
Beta strandi257 – 262Combined sources6
Beta strandi264 – 266Combined sources3
Beta strandi269 – 273Combined sources5
Beta strandi274 – 276Combined sources3
Beta strandi278 – 283Combined sources6
Beta strandi285 – 287Combined sources3
Beta strandi289 – 291Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ04491.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati7 – 46WD 1Add BLAST40
Repeati51 – 92WD 2Add BLAST42
Repeati97 – 138WD 3Add BLAST42
Repeati143 – 195WD 4Add BLAST53
Repeati202 – 244WD 5Add BLAST43
Repeati252 – 291WD 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

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31476. 151 interactors.
DIPiDIP-1826N.
IntActiQ04491. 26 interactors.
MINTiMINT-402427.

Proteomic databases

MaxQBiQ04491.
PRIDEiQ04491.

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: November 30, 2016
This is version 162 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.