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Protein

Protein transport protein Sec24D

Gene

SEC24D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 for their transport to the Golgi complex (PubMed:17499046, PubMed:20427317, PubMed:18843296). Plays a central role in cargo selection within the COPII complex and together with SEC24C may have a different specificity compared to SEC24A and SEC24B (PubMed:17499046, PubMed:20427317, PubMed:18843296). May more specifically package GPI-anchored proteins through the cargo receptor TMED10 (PubMed:20427317). May also be specific for IxM motif-containing cargos like the SNAREs GOSR2 and STX5 (PubMed:18843296).3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi363ZincCombined sources1
Metal bindingi366ZincCombined sources1
Metal bindingi385ZincCombined sources1
Metal bindingi388ZincCombined sources1

GO - Molecular functioni

  • SNARE binding Source: UniProtKB
  • zinc ion binding Source: UniProtKB

GO - Biological processi

Keywordsi

Biological processER-Golgi transport, Protein transport, Transport
LigandMetal-binding

Enzyme and pathway databases

ReactomeiR-HSA-1655829 Regulation of cholesterol biosynthesis by SREBP (SREBF)
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-2132295 MHC class II antigen presentation
R-HSA-5694530 Cargo concentration in the ER
R-HSA-983170 Antigen Presentation: Folding, assembly and peptide loading of class I MHC

Names & Taxonomyi

Protein namesi
Recommended name:
Protein transport protein Sec24DCurated
Alternative name(s):
SEC24-related protein D
Gene namesi
Name:SEC24DImported
Synonyms:KIAA0755Imported
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

EuPathDBiHostDB:ENSG00000150961.14
HGNCiHGNC:10706 SEC24D
MIMi607186 gene
neXtProtiNX_O94855

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

Cytoplasm, Cytoplasmic vesicle, Endoplasmic reticulum, Membrane

Pathology & Biotechi

Involvement in diseasei

Cole-Carpenter syndrome 2 (CLCRP2)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of Cole-Carpenter syndrome, a disorder characterized by features of osteogenesis imperfecta such as bone deformities and severe bone fragility with frequent fractures, in association with craniosynostosis, ocular proptosis, hydrocephalus, growth failure and distinctive facial features. Craniofacial findings include marked frontal bossing, midface hypoplasia, and micrognathia. Despite the craniosynostosis and hydrocephalus, intellectual development is normal. CLCRP2 inheritance is autosomal recessive.
See also OMIM:616294
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_073658978Q → P in CLCRP2. 1 PublicationCorresponds to variant dbSNP:rs786204846EnsemblClinVar.1
Natural variantiVAR_0736591015S → F in CLCRP2. 1 PublicationCorresponds to variant dbSNP:rs760670617EnsemblClinVar.1

Keywords - Diseasei

Craniosynostosis, Disease mutation, Osteogenesis imperfecta

Organism-specific databases

DisGeNETi9871
MalaCardsiSEC24D
MIMi616294 phenotype
OpenTargetsiENSG00000150961
Orphaneti2050 Cole-Carpenter syndrome
PharmGKBiPA35629

Polymorphism and mutation databases

BioMutaiSEC24D

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002051571 – 1032Protein transport protein Sec24DAdd BLAST1032

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei266PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiO94855
MaxQBiO94855
PaxDbiO94855
PeptideAtlasiO94855
PRIDEiO94855
ProteomicsDBi50488
50489 [O94855-2]

PTM databases

iPTMnetiO94855
PhosphoSitePlusiO94855
SwissPalmiO94855

Expressioni

Tissue specificityi

Ubiquitously expressed, with higher amounts in placenta, pancreas, heart and liver.1 Publication

Gene expression databases

BgeeiENSG00000150961 Expressed in 204 organ(s), highest expression level in left coronary artery
CleanExiHS_SEC24D
ExpressionAtlasiO94855 baseline and differential
GenevisibleiO94855 HS

Organism-specific databases

HPAiHPA041626
HPA053486

Interactioni

Subunit structurei

COPII is composed of at least five proteins: the Sec23/24 complex, the Sec13/31 complex and Sar1 (PubMed:17499046, PubMed:27551091). Interacts with TMED2 and TMED10 (PubMed:20427317). Interacts with CNIH4 (PubMed:24405750). Interacts with GOSR2 (via IxM motif) and STX5 (via IxM motif); recruits GOSR2 and STX5 into COPII-coated vesicles (PubMed:18843296).5 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi115204, 32 interactors
IntActiO94855, 13 interactors
MINTiO94855
STRINGi9606.ENSP00000280551

Structurei

Secondary structure

11032
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO94855
SMRiO94855
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO94855

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati901 – 974Gelsolin-likeSequence analysisAdd BLAST74

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni363 – 388Zinc finger-likeAdd BLAST26

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi10 – 293Pro-richAdd BLAST284

Sequence similaritiesi

Belongs to the SEC23/SEC24 family. SEC24 subfamily.Curated

Phylogenomic databases

eggNOGiKOG1985 Eukaryota
COG5028 LUCA
GeneTreeiENSGT00590000082962
HOGENOMiHOG000196365
HOVERGENiHBG062229
InParanoidiO94855
KOiK14007
OMAiKNKPPNP
OrthoDBiEOG091G0288
PhylomeDBiO94855
TreeFamiTF300464

Family and domain databases

Gene3Di3.40.20.10, 1 hit
3.40.50.410, 1 hit
InterProiView protein in InterPro
IPR029006 ADF-H/Gelsolin-like_dom_sf
IPR007123 Gelsolin-like_dom
IPR036180 Gelsolin-like_dom_sf
IPR006900 Sec23/24_helical_dom
IPR036175 Sec23/24_helical_dom_sf
IPR006896 Sec23/24_trunk_dom
IPR012990 Sec23_24_beta_S
IPR036465 vWFA_dom_sf
IPR006895 Znf_Sec23_Sec24
PfamiView protein in Pfam
PF00626 Gelsolin, 1 hit
PF08033 Sec23_BS, 1 hit
PF04815 Sec23_helical, 1 hit
PF04811 Sec23_trunk, 1 hit
PF04810 zf-Sec23_Sec24, 1 hit
SUPFAMiSSF53300 SSF53300, 1 hit
SSF81811 SSF81811, 1 hit
SSF82754 SSF82754, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 6 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: O94855-1) [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
MSQQGYVATP PYSQPQPGIG LSPPHYGHYG DPSHTASPTG MMKPAGPLGA
60 70 80 90 100
TATRGMLPPG PPPPGPHQFG QNGAHATGHP PQRFPGPPPV NNVASSHAPY
110 120 130 140 150
QPSAQSSYPG PISTSSVTQL GSQLSAMQIN SYGSGMAPPS QGPPGPLSAT
160 170 180 190 200
SLQTPPRPPQ PSILQPGSQV LPPPPTTLNG PGASPLPLPM YRPDGLSGPP
210 220 230 240 250
PPNAQYQPPP LPGQTLGAGY PPQQANSGPQ MAGAQLSYPG GFPGGPAQMA
260 270 280 290 300
GPPQPQKKLD PDSIPSPIQV IENDRASRGG QVYATNTRGQ IPPLVTTDCM
310 320 330 340 350
IQDQGNASPR FIRCTTYCFP CTSDMAKQAQ IPLAAVIKPF ATIPSNESPL
360 370 380 390 400
YLVNHGESGP VRCNRCKAYM CPFMQFIEGG RRYQCGFCNC VNDVPPFYFQ
410 420 430 440 450
HLDHIGRRLD HYEKPELSLG SYEYVATLDY CRKSKPPNPP AFIFMIDVSY
460 470 480 490 500
SNIKNGLVKL ICEELKTMLE KIPKEEQEET SAIRVGFITY NKVLHFFNVK
510 520 530 540 550
SNLAQPQMMV VTDVGEVFVP LLDGFLVNYQ ESQSVIHNLL DQIPDMFADS
560 570 580 590 600
NENETVFAPV IQAGMEALKA ADCPGKLFIF HSSLPTAEAP GKLKNRDDKK
610 620 630 640 650
LVNTDKEKIL FQPQTNVYDS LAKDCVAHGC SVTLFLFPSQ YVDVASLGLV
660 670 680 690 700
PQLTGGTLYK YNNFQMHLDR QQFLNDLRND IEKKIGFDAI MRVRTSTGFR
710 720 730 740 750
ATDFFGGILM NNTTDVEMAA IDCDKAVTVE FKHDDKLSED SGALIQCAVL
760 770 780 790 800
YTTISGQRRL RIHNLGLNCS SQLADLYKSC ETDALINFFA KSAFKAVLHQ
810 820 830 840 850
PLKVIREILV NQTAHMLACY RKNCASPSAA SQLILPDSMK VLPVYMNCLL
860 870 880 890 900
KNCVLLSRPE ISTDERAYQR QLVMTMGVAD SQLFFYPQLL PIHTLDVKST
910 920 930 940 950
MLPAAVRCSE SRLSEEGIFL LANGLHMFLW LGVSSPPELI QGIFNVPSFA
960 970 980 990 1000
HINTDMTLLP EVGNPYSQQL RMIMGIIQQK RPYSMKLTIV KQREQPEMVF
1010 1020 1030
RQFLVEDKGL YGGSSYVDFL CCVHKEICQL LN
Length:1,032
Mass (Da):113,010
Last modified:November 25, 2008 - v2
Checksum:iB46E566F096F37F0
GO
Isoform 2 (identifier: O94855-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     224-224: Q → QA

Note: No experimental confirmation available.
Show »
Length:1,033
Mass (Da):113,081
Checksum:i4DBA3D9F630F0043
GO

Computationally mapped potential isoform sequencesi

There are 6 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
E9PDM8E9PDM8_HUMAN
Protein transport protein Sec24D
SEC24D
663Annotation score:
E9PC44E9PC44_HUMAN
cDNA FLJ43974 fis, clone TESTI40181...
SEC24D
393Annotation score:
E9PG84E9PG84_HUMAN
Protein transport protein Sec24D
SEC24D
305Annotation score:
D6RBM1D6RBM1_HUMAN
Protein transport protein Sec24D
SEC24D
211Annotation score:
D6RGJ5D6RGJ5_HUMAN
Protein transport protein Sec24D
SEC24D
165Annotation score:
D6RAE2D6RAE2_HUMAN
Protein transport protein Sec24D
SEC24D
67Annotation score:

Sequence cautioni

The sequence BAA34475 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti559P → S in AAD28756 (PubMed:10329445).Curated1
Sequence conflicti559P → S in BAA34475 (PubMed:9872452).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04747242M → T. Corresponds to variant dbSNP:rs10029206Ensembl.1
Natural variantiVAR_047473193P → L. Corresponds to variant dbSNP:rs6844109EnsemblClinVar.1
Natural variantiVAR_047474496F → I. Corresponds to variant dbSNP:rs11723368Ensembl.1
Natural variantiVAR_073658978Q → P in CLCRP2. 1 PublicationCorresponds to variant dbSNP:rs786204846EnsemblClinVar.1
Natural variantiVAR_0736591015S → F in CLCRP2. 1 PublicationCorresponds to variant dbSNP:rs760670617EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_035761224Q → QA in isoform 2. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF130464 mRNA Translation: AAD28756.2
AB018298 mRNA Translation: BAA34475.2 Different initiation.
CH471229 Genomic DNA Translation: EAW73656.1
BC035761 mRNA Translation: AAH35761.1
CCDSiCCDS3710.1 [O94855-1]
RefSeqiNP_001304995.1, NM_001318066.1 [O94855-2]
NP_055637.2, NM_014822.3 [O94855-1]
XP_005263436.1, XM_005263379.2 [O94855-2]
UniGeneiHs.189641

Genome annotation databases

EnsembliENST00000280551; ENSP00000280551; ENSG00000150961 [O94855-1]
GeneIDi9871
KEGGihsa:9871
UCSCiuc003ici.5 human [O94855-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF130464 mRNA Translation: AAD28756.2
AB018298 mRNA Translation: BAA34475.2 Different initiation.
CH471229 Genomic DNA Translation: EAW73656.1
BC035761 mRNA Translation: AAH35761.1
CCDSiCCDS3710.1 [O94855-1]
RefSeqiNP_001304995.1, NM_001318066.1 [O94855-2]
NP_055637.2, NM_014822.3 [O94855-1]
XP_005263436.1, XM_005263379.2 [O94855-2]
UniGeneiHs.189641

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3EFOX-ray2.70B266-1032[»]
3EG9X-ray3.00B266-1032[»]
5KYUX-ray3.51B266-1032[»]
5KYWX-ray3.20B266-1032[»]
5KYXX-ray3.52B266-1032[»]
5KYYX-ray3.40B266-1032[»]
ProteinModelPortaliO94855
SMRiO94855
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115204, 32 interactors
IntActiO94855, 13 interactors
MINTiO94855
STRINGi9606.ENSP00000280551

PTM databases

iPTMnetiO94855
PhosphoSitePlusiO94855
SwissPalmiO94855

Polymorphism and mutation databases

BioMutaiSEC24D

Proteomic databases

EPDiO94855
MaxQBiO94855
PaxDbiO94855
PeptideAtlasiO94855
PRIDEiO94855
ProteomicsDBi50488
50489 [O94855-2]

Protocols and materials databases

DNASUi9871
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000280551; ENSP00000280551; ENSG00000150961 [O94855-1]
GeneIDi9871
KEGGihsa:9871
UCSCiuc003ici.5 human [O94855-1]

Organism-specific databases

CTDi9871
DisGeNETi9871
EuPathDBiHostDB:ENSG00000150961.14
GeneCardsiSEC24D
H-InvDBiHIX0004459
HGNCiHGNC:10706 SEC24D
HPAiHPA041626
HPA053486
MalaCardsiSEC24D
MIMi607186 gene
616294 phenotype
neXtProtiNX_O94855
OpenTargetsiENSG00000150961
Orphaneti2050 Cole-Carpenter syndrome
PharmGKBiPA35629
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1985 Eukaryota
COG5028 LUCA
GeneTreeiENSGT00590000082962
HOGENOMiHOG000196365
HOVERGENiHBG062229
InParanoidiO94855
KOiK14007
OMAiKNKPPNP
OrthoDBiEOG091G0288
PhylomeDBiO94855
TreeFamiTF300464

Enzyme and pathway databases

ReactomeiR-HSA-1655829 Regulation of cholesterol biosynthesis by SREBP (SREBF)
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-2132295 MHC class II antigen presentation
R-HSA-5694530 Cargo concentration in the ER
R-HSA-983170 Antigen Presentation: Folding, assembly and peptide loading of class I MHC

Miscellaneous databases

ChiTaRSiSEC24D human
EvolutionaryTraceiO94855
GeneWikiiSEC24D
GenomeRNAii9871
PROiPR:O94855
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000150961 Expressed in 204 organ(s), highest expression level in left coronary artery
CleanExiHS_SEC24D
ExpressionAtlasiO94855 baseline and differential
GenevisibleiO94855 HS

Family and domain databases

Gene3Di3.40.20.10, 1 hit
3.40.50.410, 1 hit
InterProiView protein in InterPro
IPR029006 ADF-H/Gelsolin-like_dom_sf
IPR007123 Gelsolin-like_dom
IPR036180 Gelsolin-like_dom_sf
IPR006900 Sec23/24_helical_dom
IPR036175 Sec23/24_helical_dom_sf
IPR006896 Sec23/24_trunk_dom
IPR012990 Sec23_24_beta_S
IPR036465 vWFA_dom_sf
IPR006895 Znf_Sec23_Sec24
PfamiView protein in Pfam
PF00626 Gelsolin, 1 hit
PF08033 Sec23_BS, 1 hit
PF04815 Sec23_helical, 1 hit
PF04811 Sec23_trunk, 1 hit
PF04810 zf-Sec23_Sec24, 1 hit
SUPFAMiSSF53300 SSF53300, 1 hit
SSF81811 SSF81811, 1 hit
SSF82754 SSF82754, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSC24D_HUMAN
AccessioniPrimary (citable) accession number: O94855
Secondary accession number(s): Q8IYI7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 21, 2001
Last sequence update: November 25, 2008
Last modified: November 7, 2018
This is version 159 of the entry and version 2 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, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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