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Protein

Transmembrane emp24 domain-containing protein 10

Gene

Tmed10

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in vesicular protein trafficking. Mainly functions in the early secretory pathway. Thought to act as cargo receptor at the lumenal side for incorporation of secretory cargo molecules into transport vesicles and to be involved in vesicle coat formation at the cytoplasmic side. In COPII vesicle-mediated anterograde transport involved in the transport of GPI-anchored proteins and proposed to act together with TMED2 as their cargo receptor; the function specifically implies SEC24C and SEC24D of the COPII vesicle coat and lipid raft-like microdomains of the ER. Recognizes GPI anchors structural remodeled in the ER by PGAP1 and MPPE1. In COPI vesicle-mediated retrograde transport involved in the biogenesis of COPI vesicles and vesicle coat recruitment. On Golgi membranes, acts as primary receptor for ARF1-GDP which is involved in COPI-vesicle formation. Increases coatomer-dependent GTPase-activating activity of ARFGAP2. Involved in trafficking of G protein-coupled receptors (GPCRs). Regulates F2LR1, OPRM1 and P2RY4 exocytic trafficking from the Golgi to the plasma membrane thus contributing to receptor resensitization. Involved in trafficking of amyloid beta A4 protein and soluble APP-beta release (independent of modulation of gamma-secretase activity). As part of the presenilin-dependent gamma-secretase complex regulates gamma-cleavages of the amyloid beta A4 protein to yield amyloid-beta 40 (Abeta40). Involved in organization of the Golgi apparatus (By similarity).By similarity

GO - Molecular functioni

  • protein complex binding Source: RGD

GO - Biological processi

  • COPI-coated vesicle budding Source: UniProtKB
  • Golgi organization Source: RGD
  • intracellular protein transport Source: HGNC
  • kidney development Source: RGD
  • protein oligomerization Source: RGD
  • regulated exocytosis Source: HGNC
  • regulation of beta-amyloid formation Source: UniProtKB
  • response to alkaloid Source: RGD
  • retrograde vesicle-mediated transport, Golgi to ER Source: UniProtKB
  • vesicle targeting Source: HGNC
  • vesicle targeting, to, from or within Golgi Source: HGNC
Complete GO annotation...

Keywords - Biological processi

ER-Golgi transport, Protein transport, Transport

Enzyme and pathway databases

ReactomeiR-RNO-204005. COPII (Coat Protein 2) Mediated Vesicle Transport.
R-RNO-5694530. Cargo concentration in the ER.
R-RNO-6807878. COPI-mediated anterograde transport.
R-RNO-6811434. COPI-dependent Golgi-to-ER retrograde traffic.

Names & Taxonomyi

Protein namesi
Recommended name:
Transmembrane emp24 domain-containing protein 10
Alternative name(s):
21 kDa transmembrane-trafficking protein
Transmembrane protein Tmp21
p24 family protein delta-1
Short name:
p24delta1
Gene namesi
Name:Tmed10
Synonyms:Tmp21
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 6

Organism-specific databases

RGDi620970. Tmed10.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini32 – 185LumenalSequence analysisAdd BLAST154
Transmembranei186 – 206HelicalSequence analysisAdd BLAST21
Topological domaini207 – 219CytoplasmicSequence analysisAdd BLAST13

GO - Cellular componenti

  • cis-Golgi network Source: HGNC
  • COPI-coated vesicle Source: RGD
  • endoplasmic reticulum-Golgi intermediate compartment Source: RGD
  • endoplasmic reticulum-Golgi intermediate compartment membrane Source: UniProtKB-SubCell
  • endoplasmic reticulum membrane Source: UniProtKB-SubCell
  • extracellular exosome Source: Ensembl
  • gamma-secretase complex Source: RGD
  • Golgi membrane Source: GOC
  • integral component of membrane Source: HGNC
  • intracellular membrane-bounded organelle Source: RGD
  • melanosome Source: UniProtKB-SubCell
  • plasma membrane Source: UniProtKB
  • secretory granule membrane Source: UniProtKB
  • trans-Golgi network transport vesicle Source: UniProtKB
  • transport vesicle membrane Source: UniProtKB-SubCell
  • zymogen granule membrane Source: HGNC
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cytoplasmic vesicle, Endoplasmic reticulum, Golgi apparatus, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi215 – 216KK → SS: Reduced localization to COPI-coated vesicles and endoplasmic reticulum-Golgi intermediate compartment. 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 31By similarityAdd BLAST31
ChainiPRO_000001040432 – 219Transmembrane emp24 domain-containing protein 10Add BLAST188

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei171Dimethylated arginine1 Publication1
Modified residuei176Dimethylated arginine1 Publication1
Glycosylationi179N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Glycoprotein, Methylation

Proteomic databases

PaxDbiQ63584.
PRIDEiQ63584.

PTM databases

iPTMnetiQ63584.
PhosphoSitePlusiQ63584.
SwissPalmiQ63584.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiENSRNOG00000007901.
GenevisibleiQ63584. RN.

Interactioni

Subunit structurei

Predominantly homodimeric and to lesser extent monomeric in endoplasmic reticulum. Homodimer and monomer in endoplasmic reticulum-Golgi intermediate compartment and cis-Golgi network. Probably oligomerizes with other members of the EMP24/GP25L family such as TMED2, TMED7 and TMED9. Interacts with TMED2. Associates with the COPI vesicle coat (coatomer); TMED10:TMED2 heterotetramers are proposed to be involved in coatomer association. Interacts (via C-terminus) with COPG1; the interaction involves dimeric TMED10. Interacts with ARF1 (GDP-bound); the interaction probably involves a TMED10 oligomer. Interacts with SEC23A; indicative for an association of TMED10 with the COPII vesicle coat. Interacts with CD59, SEC24B, SEC24C and SEC24D. Interacts with MPPE1/PGAP5. Interacts with F2LR1. Interacts with KDELR2; the interaction is disrupted by KDELR2 ligand. Found in a complex composed at least of SURF4, TMED2 and TMED10. Associates with the presenilin-dependent gamma-secretase complex (By similarity). Interacts with STX17; the interaction is direct.By similarity4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Gorasp2Q9R0642EBI-918648,EBI-4422912

GO - Molecular functioni

  • protein complex binding Source: RGD

Protein-protein interaction databases

BioGridi250029. 1 interactor.
IntActiQ63584. 7 interactors.
MINTiMINT-4579083.
STRINGi10116.ENSRNOP00000010512.

Structurei

Secondary structure

1219
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi32 – 36Combined sources5
Beta strandi41 – 47Combined sources7
Beta strandi53 – 61Combined sources9
Helixi67 – 69Combined sources3
Beta strandi71 – 78Combined sources8
Beta strandi83 – 89Combined sources7
Beta strandi91 – 98Combined sources8
Beta strandi104 – 112Combined sources9
Beta strandi120 – 128Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5AZXX-ray1.58A/B/C/D32-132[»]
5AZYX-ray1.80A/B32-132[»]
SMRiQ63584.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini41 – 193GOLDPROSITE-ProRule annotationAdd BLAST153

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 142Required for interaction with STX17By similarityAdd BLAST142
Regioni147 – 178Required for TMED10 and TMED2 cis-Golgi network localizationBy similarityAdd BLAST32
Regioni204 – 219Interaction with COPG1By similarityAdd BLAST16
Regioni207 – 219Interaction with ARF1By similarityAdd BLAST13

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi211 – 219COPI vesicle coat-bindingSequence analysis9
Motifi211 – 212COPII vesicle coat-bindingSequence analysis2

Domaini

The lumenal domain mediates localization to the plasma membrane by partially overriding the ER retention by the cytoplasmic domain.

Sequence similaritiesi

Belongs to the EMP24/GP25L family.Curated
Contains 1 GOLD domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG1691. Eukaryota.
ENOG410XTBQ. LUCA.
GeneTreeiENSGT00550000074954.
HOVERGENiHBG107275.
InParanoidiQ63584.
KOiK20352.
OMAiHTLYSKE.
OrthoDBiEOG091G0O9D.
PhylomeDBiQ63584.

Family and domain databases

InterProiIPR009038. GOLD_dom.
IPR015720. TMP21-related.
[Graphical view]
PANTHERiPTHR22811. PTHR22811. 1 hit.
PfamiPF01105. EMP24_GP25L. 1 hit.
[Graphical view]
SMARTiSM01190. EMP24_GP25L. 1 hit.
[Graphical view]
PROSITEiPS50866. GOLD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q63584-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGLSGPLSW PGPLLSALLF LFLLGPSSVL GISFHLPVNS RKCLREEIHK
60 70 80 90 100
DLLVTGAYEI TDQSGGAGGL RTHLKITDSA GHILYAKEDA TKGKFAFTTE
110 120 130 140 150
DYDMFEVCFE SKGTGRIPDQ LVILDMKHGV EAKNYEEIAK VEKLKPLEVE
160 170 180 190 200
LRRLEDLSES IVNDFAYMKK REEEMRDTNE STNTRVLYFS IFSMFCLIGL
210
ATWQVFYLRR FFKAKKLIE
Length:219
Mass (Da):24,858
Last modified:April 26, 2005 - v2
Checksum:i51FC99ECB6D47ADE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ004912 mRNA. Translation: CAA06212.1.
X97443 mRNA. Translation: CAA66072.1.
RefSeqiNP_445919.1. NM_053467.1.
UniGeneiRn.226085.
Rn.8509.

Genome annotation databases

EnsembliENSRNOT00000010512; ENSRNOP00000010512; ENSRNOG00000007901.
GeneIDi84599.
KEGGirno:84599.
UCSCiRGD:620970. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ004912 mRNA. Translation: CAA06212.1.
X97443 mRNA. Translation: CAA66072.1.
RefSeqiNP_445919.1. NM_053467.1.
UniGeneiRn.226085.
Rn.8509.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5AZXX-ray1.58A/B/C/D32-132[»]
5AZYX-ray1.80A/B32-132[»]
SMRiQ63584.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi250029. 1 interactor.
IntActiQ63584. 7 interactors.
MINTiMINT-4579083.
STRINGi10116.ENSRNOP00000010512.

PTM databases

iPTMnetiQ63584.
PhosphoSitePlusiQ63584.
SwissPalmiQ63584.

Proteomic databases

PaxDbiQ63584.
PRIDEiQ63584.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000010512; ENSRNOP00000010512; ENSRNOG00000007901.
GeneIDi84599.
KEGGirno:84599.
UCSCiRGD:620970. rat.

Organism-specific databases

CTDi10972.
RGDi620970. Tmed10.

Phylogenomic databases

eggNOGiKOG1691. Eukaryota.
ENOG410XTBQ. LUCA.
GeneTreeiENSGT00550000074954.
HOVERGENiHBG107275.
InParanoidiQ63584.
KOiK20352.
OMAiHTLYSKE.
OrthoDBiEOG091G0O9D.
PhylomeDBiQ63584.

Enzyme and pathway databases

ReactomeiR-RNO-204005. COPII (Coat Protein 2) Mediated Vesicle Transport.
R-RNO-5694530. Cargo concentration in the ER.
R-RNO-6807878. COPI-mediated anterograde transport.
R-RNO-6811434. COPI-dependent Golgi-to-ER retrograde traffic.

Miscellaneous databases

PROiQ63584.

Gene expression databases

BgeeiENSRNOG00000007901.
GenevisibleiQ63584. RN.

Family and domain databases

InterProiIPR009038. GOLD_dom.
IPR015720. TMP21-related.
[Graphical view]
PANTHERiPTHR22811. PTHR22811. 1 hit.
PfamiPF01105. EMP24_GP25L. 1 hit.
[Graphical view]
SMARTiSM01190. EMP24_GP25L. 1 hit.
[Graphical view]
PROSITEiPS50866. GOLD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTMEDA_RAT
AccessioniPrimary (citable) accession number: Q63584
Secondary accession number(s): Q9R0W6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: April 26, 2005
Last modified: November 30, 2016
This is version 116 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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

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.