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Protein

Ras-related protein Rab-3D

Gene

RAB3D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Protein transport. Probably involved in regulated exocytosis (By similarity).By similarity

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi29 – 37GTPCombined sources9
Nucleotide bindingi48 – 54GTPBy similarity7
Nucleotide bindingi77 – 81GTPBy similarity5
Nucleotide bindingi135 – 138GTPCombined sources4
Nucleotide bindingi165 – 167GTPCombined sources3

GO - Molecular functioni

  • GTPase activity Source: GO_Central
  • GTP binding Source: UniProtKB-KW
  • GTP-dependent protein binding Source: Ensembl
  • myosin V binding Source: UniProtKB

GO - Biological processi

Keywordsi

Biological processExocytosis, Protein transport, Transport
LigandGTP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-6798695 Neutrophil degranulation
R-HSA-8873719 RAB geranylgeranylation

Names & Taxonomyi

Protein namesi
Recommended name:
Ras-related protein Rab-3D
Gene namesi
Name:RAB3D
Synonyms:GOV, RAB16
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

EuPathDBiHostDB:ENSG00000105514.7
HGNCiHGNC:9779 RAB3D
MIMi604350 gene
neXtProtiNX_O95716

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

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi9545
OpenTargetsiENSG00000105514
PharmGKBiPA34134

Polymorphism and mutation databases

BioMutaiRAB3D

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001210882 – 219Ras-related protein Rab-3DAdd BLAST218

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei190PhosphoserineBy similarity1
Lipidationi217S-geranylgeranyl cysteineBy similarity1
Modified residuei219Cysteine methyl esterBy similarity1
Lipidationi219S-geranylgeranyl cysteineBy similarity1

Keywords - PTMi

Acetylation, Lipoprotein, Methylation, Phosphoprotein, Prenylation

Proteomic databases

EPDiO95716
MaxQBiO95716
PaxDbiO95716
PeptideAtlasiO95716
PRIDEiO95716
ProteomicsDBi51010

PTM databases

iPTMnetiO95716
PhosphoSitePlusiO95716
SwissPalmiO95716

Expressioni

Tissue specificityi

Highly expressed in granulocytes of peripheral blood. Constitutively expressed at low levels in all hematopoietic cell lines investigated.

Inductioni

Activated in myeloid differentiation.

Gene expression databases

BgeeiENSG00000105514 Expressed in 200 organ(s), highest expression level in saliva-secreting gland
CleanExiHS_RAB3D
ExpressionAtlasiO95716 baseline and differential
GenevisibleiO95716 HS

Organism-specific databases

HPAiCAB018067
HPA063283

Interactioni

Subunit structurei

Interacts with RIMS1, RIMS2, RPH3A, RPH3AL and RAB3IP.By similarity

GO - Molecular functioni

Protein-protein interaction databases

BioGridi114919, 9 interactors
IntActiO95716, 6 interactors
STRINGi9606.ENSP00000222120

Structurei

Secondary structure

1219
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO95716
SMRiO95716
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO95716

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi51 – 59Effector regionBy similarity9

Sequence similaritiesi

Belongs to the small GTPase superfamily. Rab family.Curated

Phylogenomic databases

eggNOGiKOG0093 Eukaryota
ENOG410ZZXQ LUCA
GeneTreeiENSGT00890000139330
HOGENOMiHOG000233968
HOVERGENiHBG009351
InParanoidiO95716
KOiK07884
OMAiKGPTLGD
OrthoDBiEOG091G0J64
PhylomeDBiO95716
TreeFamiTF313199

Family and domain databases

CDDicd01865 Rab3, 1 hit
InterProiView protein in InterPro
IPR027417 P-loop_NTPase
IPR037872 Rab3
IPR005225 Small_GTP-bd_dom
IPR001806 Small_GTPase
PfamiView protein in Pfam
PF00071 Ras, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit
TIGRFAMsiTIGR00231 small_GTP, 1 hit
PROSITEiView protein in PROSITE
PS51419 RAB, 1 hit

Sequencei

Sequence statusi: Complete.

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

O95716-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MASAGDTQAG PRDAADQNFD YMFKLLLIGN SSVGKTSFLF RYADDSFTPA
60 70 80 90 100
FVSTVGIDFK VKTVYRHDKR IKLQIWDTAG QERYRTITTA YYRGAMGFLL
110 120 130 140 150
MYDIANQESF AAVQDWATQI KTYSWDNAQV ILVGNKCDLE DERVVPAEDG
160 170 180 190 200
RRLADDLGFE FFEASAKENI NVKQVFERLV DVICEKMNES LEPSSSSGSN
210
GKGPAVGDAP APQPSSCSC
Length:219
Mass (Da):24,267
Last modified:May 1, 1999 - v1
Checksum:i714754826C405EA7
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05171064V → I. Corresponds to variant dbSNP:rs3969860Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF081353 mRNA Translation: AAC72918.1
AF498933 mRNA Translation: AAM21081.1
BC016471 mRNA Translation: AAH16471.1
CCDSiCCDS12257.1
RefSeqiNP_004274.1, NM_004283.3
UniGeneiHs.744916

Genome annotation databases

EnsembliENST00000222120; ENSP00000222120; ENSG00000105514
ENST00000589655; ENSP00000466000; ENSG00000105514
GeneIDi9545
KEGGihsa:9545
UCSCiuc002mqx.3 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF081353 mRNA Translation: AAC72918.1
AF498933 mRNA Translation: AAM21081.1
BC016471 mRNA Translation: AAH16471.1
CCDSiCCDS12257.1
RefSeqiNP_004274.1, NM_004283.3
UniGeneiHs.744916

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2GF9X-ray1.53A20-189[»]
ProteinModelPortaliO95716
SMRiO95716
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114919, 9 interactors
IntActiO95716, 6 interactors
STRINGi9606.ENSP00000222120

PTM databases

iPTMnetiO95716
PhosphoSitePlusiO95716
SwissPalmiO95716

Polymorphism and mutation databases

BioMutaiRAB3D

Proteomic databases

EPDiO95716
MaxQBiO95716
PaxDbiO95716
PeptideAtlasiO95716
PRIDEiO95716
ProteomicsDBi51010

Protocols and materials databases

DNASUi9545
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000222120; ENSP00000222120; ENSG00000105514
ENST00000589655; ENSP00000466000; ENSG00000105514
GeneIDi9545
KEGGihsa:9545
UCSCiuc002mqx.3 human

Organism-specific databases

CTDi9545
DisGeNETi9545
EuPathDBiHostDB:ENSG00000105514.7
GeneCardsiRAB3D
HGNCiHGNC:9779 RAB3D
HPAiCAB018067
HPA063283
MIMi604350 gene
neXtProtiNX_O95716
OpenTargetsiENSG00000105514
PharmGKBiPA34134
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0093 Eukaryota
ENOG410ZZXQ LUCA
GeneTreeiENSGT00890000139330
HOGENOMiHOG000233968
HOVERGENiHBG009351
InParanoidiO95716
KOiK07884
OMAiKGPTLGD
OrthoDBiEOG091G0J64
PhylomeDBiO95716
TreeFamiTF313199

Enzyme and pathway databases

ReactomeiR-HSA-6798695 Neutrophil degranulation
R-HSA-8873719 RAB geranylgeranylation

Miscellaneous databases

ChiTaRSiRAB3D human
EvolutionaryTraceiO95716
GeneWikiiRAB3D
GenomeRNAii9545
PROiPR:O95716
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000105514 Expressed in 200 organ(s), highest expression level in saliva-secreting gland
CleanExiHS_RAB3D
ExpressionAtlasiO95716 baseline and differential
GenevisibleiO95716 HS

Family and domain databases

CDDicd01865 Rab3, 1 hit
InterProiView protein in InterPro
IPR027417 P-loop_NTPase
IPR037872 Rab3
IPR005225 Small_GTP-bd_dom
IPR001806 Small_GTPase
PfamiView protein in Pfam
PF00071 Ras, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit
TIGRFAMsiTIGR00231 small_GTP, 1 hit
PROSITEiView protein in PROSITE
PS51419 RAB, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRAB3D_HUMAN
AccessioniPrimary (citable) accession number: O95716
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: May 1, 1999
Last modified: November 7, 2018
This is version 173 of the entry and version 1 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 entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  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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