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Protein

Ras-related protein Rab-3D

Gene

RAB3D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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: ProtInc
  • GTP binding Source: UniProtKB-KW
  • myosin V binding Source: UniProtKB

GO - Biological processi

  • bone resorption Source: GO_Central
  • exocytosis Source: UniProtKB-KW
  • peptidyl-cysteine methylation Source: Ensembl
  • positive regulation of regulated secretory pathway Source: UniProtKB
  • protein transport Source: UniProtKB-KW
  • small GTPase mediated signal transduction Source: InterPro
Complete GO annotation...

Keywords - Biological processi

Exocytosis, Protein transport, Transport

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000105514-MONOMER.
ReactomeiR-HSA-6798695. Neutrophil degranulation.

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

HGNCiHGNC:9779. RAB3D.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic microtubule Source: GO_Central
  • extracellular exosome Source: UniProtKB
  • mitochondrion Source: Ensembl
  • plasma membrane Source: UniProtKB-SubCell
  • secretory vesicle Source: GO_Central
  • transport vesicle Source: Ensembl
  • zymogen granule Source: Ensembl
Complete GO annotation...

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
Lipidationi217S-geranylgeranyl cysteineBy similarity1
Modified residuei219Cysteine methyl esterBy similarity1
Lipidationi219S-geranylgeranyl cysteineBy similarity1

Keywords - PTMi

Acetylation, Lipoprotein, Methylation, Prenylation

Proteomic databases

EPDiO95716.
MaxQBiO95716.
PaxDbiO95716.
PeptideAtlasiO95716.
PRIDEiO95716.

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.
CleanExiHS_RAB3D.
ExpressionAtlasiO95716. baseline and differential.
GenevisibleiO95716. HS.

Organism-specific databases

HPAiCAB018067.
HPA051912.

Interactioni

Subunit structurei

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

GO - Molecular functioni

  • myosin V binding Source: UniProtKB

Protein-protein interaction databases

BioGridi114919. 8 interactors.
IntActiO95716. 4 interactors.
STRINGi9606.ENSP00000222120.

Structurei

Secondary structure

1219
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi20 – 28Combined sources9
Helixi35 – 44Combined sources10
Beta strandi58 – 66Combined sources9
Beta strandi69 – 77Combined sources9
Helixi88 – 92Combined sources5
Beta strandi96 – 103Combined sources8
Helixi107 – 111Combined sources5
Helixi113 – 123Combined sources11
Beta strandi129 – 135Combined sources7
Helixi140 – 142Combined sources3
Helixi147 – 157Combined sources11
Beta strandi160 – 163Combined sources4
Turni166 – 169Combined sources4
Helixi172 – 187Combined sources16

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...

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.
GeneTreeiENSGT00860000133677.
HOGENOMiHOG000233968.
HOVERGENiHBG009351.
InParanoidiO95716.
KOiK07884.
OMAiEPSSCSC.
OrthoDBiEOG091G0J64.
PhylomeDBiO95716.
TreeFamiTF313199.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
[Graphical view]
PfamiPF00071. Ras. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51419. RAB. 1 hit.
[Graphical view]

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 rs3969860dbSNPEnsembl.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

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. 8 interactors.
IntActiO95716. 4 interactors.
STRINGi9606.ENSP00000222120.

PTM databases

iPTMnetiO95716.
PhosphoSitePlusiO95716.
SwissPalmiO95716.

Polymorphism and mutation databases

BioMutaiRAB3D.

Proteomic databases

EPDiO95716.
MaxQBiO95716.
PaxDbiO95716.
PeptideAtlasiO95716.
PRIDEiO95716.

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.
GeneCardsiRAB3D.
HGNCiHGNC:9779. RAB3D.
HPAiCAB018067.
HPA051912.
MIMi604350. gene.
neXtProtiNX_O95716.
OpenTargetsiENSG00000105514.
PharmGKBiPA34134.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0093. Eukaryota.
ENOG410ZZXQ. LUCA.
GeneTreeiENSGT00860000133677.
HOGENOMiHOG000233968.
HOVERGENiHBG009351.
InParanoidiO95716.
KOiK07884.
OMAiEPSSCSC.
OrthoDBiEOG091G0J64.
PhylomeDBiO95716.
TreeFamiTF313199.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000105514-MONOMER.
ReactomeiR-HSA-6798695. Neutrophil degranulation.

Miscellaneous databases

EvolutionaryTraceiO95716.
GeneWikiiRAB3D.
GenomeRNAii9545.
PROiO95716.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000105514.
CleanExiHS_RAB3D.
ExpressionAtlasiO95716. baseline and differential.
GenevisibleiO95716. HS.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
[Graphical view]
PfamiPF00071. Ras. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51419. RAB. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRAB3D_HUMAN
AccessioniPrimary (citable) accession number: O95716
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: May 1, 1999
Last modified: November 30, 2016
This is version 159 of the entry and version 1 of the sequence. [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. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.