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Protein

Protein transport protein SEC13

Gene

SEC13

Organism
Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) (Pichia pastoris)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. 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 (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

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

Names & Taxonomyi

Protein namesi
Recommended name:
Protein transport protein SEC13
Gene namesi
Name:SEC13
Ordered Locus Names:PAS_chr1-3_0057
OrganismiKomagataella phaffii (strain GS115 / ATCC 20864) (Yeast) (Pichia pastoris)
Taxonomic identifieri644223 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesPhaffomycetaceaeKomagataella
Proteomesi
  • UP000000314 Componenti: Chromosome 1

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000512051 – 289Protein transport protein SEC13Add BLAST289

Interactioni

Subunit structurei

The COPII coat is composed of at least 5 proteins: the SEC23/24 complex, the SEC13/31 complex, and the protein SAR1. Also component of the nuclear pore (By similarity).By similarity

Protein-protein interaction databases

IntActiP53024. 5 interactors.
MINTiMINT-3370733.
STRINGi644223.XP_002489393.1.

Structurei

Secondary structure

1289
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 5Combined sources4
Beta strandi8 – 10Combined sources3
Beta strandi12 – 17Combined sources6
Beta strandi21 – 28Combined sources8
Beta strandi31 – 39Combined sources9
Beta strandi42 – 50Combined sources9
Beta strandi56 – 61Combined sources6
Helixi64 – 66Combined sources3
Beta strandi68 – 74Combined sources7
Beta strandi79 – 87Combined sources9
Beta strandi89 – 95Combined sources7
Beta strandi102 – 107Combined sources6
Helixi110 – 112Combined sources3
Beta strandi114 – 120Combined sources7
Beta strandi123 – 129Combined sources7
Beta strandi139 – 142Combined sources4
Beta strandi148 – 153Combined sources6
Beta strandi164 – 169Combined sources6
Beta strandi174 – 180Combined sources7
Turni181 – 184Combined sources4
Beta strandi185 – 192Combined sources8
Beta strandi199 – 204Combined sources6
Beta strandi209 – 218Combined sources10
Beta strandi223 – 228Combined sources6
Beta strandi235 – 240Combined sources6
Beta strandi249 – 254Combined sources6
Beta strandi256 – 258Combined sources3
Beta strandi261 – 265Combined sources5
Beta strandi270 – 275Combined sources6
Beta strandi281 – 286Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4L9OX-ray1.60A/B2-289[»]
ProteinModelPortaliP53024.
SMRiP53024.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati7 – 37WD 1Add BLAST31
Repeati51 – 83WD 2Add BLAST33
Repeati97 – 131WD 3Add BLAST35
Repeati147 – 178WD 4Add BLAST32
Repeati197 – 227WD 5Add BLAST31
Repeati244 – 274WD 6Add BLAST31

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.
HOGENOMiHOG000216895.
InParanoidiP53024.
KOiK14004.
OMAiDHVTFPA.
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. 3 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.

P53024-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVTIGNAHDD LIHDAVLDYY GRRLATCSSD KTIKIFEIDG ENQRLVETLI
60 70 80 90 100
GHEGPVWQVA WAHPKFGVIL ASCSYDGKVL IWKEDNGVWN KVAEHSVHQA
110 120 130 140 150
SVNSVSWAPH EYGPVLLCAS SDGKISIVEF KDGGALEPIV IQGHAIGVNA
160 170 180 190 200
ASWAPISLPD NTRRFVSGGC DNLVKIWRYD DAAKTFIEEE AFQGHSDWVR
210 220 230 240 250
DVAWSPSRLS KSYIATASQD RTVLIWTKDG KSNKWEKQPL TKEKFPDVCW
260 270 280
RASWSLSGNV LAISGGDNKV TLWKENIQGK WESAGEVDQ
Length:289
Mass (Da):32,105
Last modified:September 1, 2009 - v3
Checksum:iC711A2810ED1F049
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti148V → G in AAB01155 (PubMed:10923020).Curated1
Sequence conflicti273W → S in AAB01155 (PubMed:10923020).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U52430 Genomic DNA. Translation: AAB01155.2.
FN392319 Genomic DNA. Translation: CAY67109.1.
PIRiT10477.
RefSeqiXP_002489393.1. XM_002489348.1.

Genome annotation databases

EnsemblFungiiCAY67109; CAY67109; PAS_chr1-3_0057.
GeneIDi8197368.
KEGGippa:PAS_chr1-3_0057.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U52430 Genomic DNA. Translation: AAB01155.2.
FN392319 Genomic DNA. Translation: CAY67109.1.
PIRiT10477.
RefSeqiXP_002489393.1. XM_002489348.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4L9OX-ray1.60A/B2-289[»]
ProteinModelPortaliP53024.
SMRiP53024.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP53024. 5 interactors.
MINTiMINT-3370733.
STRINGi644223.XP_002489393.1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCAY67109; CAY67109; PAS_chr1-3_0057.
GeneIDi8197368.
KEGGippa:PAS_chr1-3_0057.

Phylogenomic databases

eggNOGiKOG1332. Eukaryota.
ENOG410XPFM. LUCA.
HOGENOMiHOG000216895.
InParanoidiP53024.
KOiK14004.
OMAiDHVTFPA.
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. 3 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_KOMPG
AccessioniPrimary (citable) accession number: P53024
Secondary accession number(s): C4QV39
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: September 1, 2009
Last modified: November 30, 2016
This is version 115 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.