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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)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi29 – 379GTP
Nucleotide bindingi77 – 815GTPBy similarity
Nucleotide bindingi135 – 1384GTP
Nucleotide bindingi165 – 1673GTP

GO - Molecular functioni

  1. GDP binding Source: GO_Central
  2. GTPase activity Source: ProtInc
  3. GTP binding Source: GO_Central
  4. myosin V binding Source: UniProtKB

GO - Biological processi

  1. intracellular protein transport Source: GO_Central
  2. peptidyl-cysteine methylation Source: Ensembl
  3. positive regulation of regulated secretory pathway Source: UniProtKB
  4. protein secretion Source: GO_Central
  5. Rab protein signal transduction Source: GO_Central
  6. regulation of exocytosis Source: GO_Central
  7. synaptic vesicle exocytosis Source: GO_Central
  8. vesicle docking involved in exocytosis Source: GO_Central
Complete GO annotation...

Keywords - Biological processi

Exocytosis, Protein transport, Transport

Keywords - Ligandi

GTP-binding, Nucleotide-binding

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
ProteomesiUP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:9779. RAB3D.

Subcellular locationi

Cell membrane Curated; Lipid-anchor Curated; Cytoplasmic side Curated

GO - Cellular componenti

  1. endosome Source: GO_Central
  2. extracellular vesicular exosome Source: UniProtKB
  3. mitochondrion Source: Ensembl
  4. plasma membrane Source: GO_Central
  5. secretory granule membrane Source: GO_Central
  6. synaptic vesicle Source: GO_Central
  7. transport vesicle Source: Ensembl
  8. zymogen granule Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA34134.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 219218Ras-related protein Rab-3DPRO_0000121088Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine1 Publication
Lipidationi217 – 2171S-geranylgeranyl cysteineBy similarity
Modified residuei219 – 2191Cysteine methyl esterBy similarity
Lipidationi219 – 2191S-geranylgeranyl cysteineBy similarity

Keywords - PTMi

Acetylation, Lipoprotein, Methylation, Prenylation

Proteomic databases

MaxQBiO95716.
PaxDbiO95716.
PRIDEiO95716.

PTM databases

PhosphoSiteiO95716.

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

BgeeiO95716.
CleanExiHS_RAB3D.
ExpressionAtlasiO95716. baseline and differential.
GenevestigatoriO95716.

Organism-specific databases

HPAiCAB018067.
HPA051912.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi114919. 12 interactions.
IntActiO95716. 3 interactions.
STRINGi9606.ENSP00000222120.

Structurei

Secondary structure

1
219
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi20 – 289Combined sources
Helixi35 – 4410Combined sources
Beta strandi58 – 669Combined sources
Beta strandi69 – 779Combined sources
Helixi88 – 925Combined sources
Beta strandi96 – 1038Combined sources
Helixi107 – 1115Combined sources
Helixi113 – 12311Combined sources
Beta strandi129 – 1357Combined sources
Helixi140 – 1423Combined sources
Helixi147 – 15711Combined sources
Beta strandi160 – 1634Combined sources
Turni166 – 1694Combined sources
Helixi172 – 18716Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2GF9X-ray1.53A20-189[»]
ProteinModelPortaliO95716.
SMRiO95716. Positions 20-189.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO95716.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi51 – 599Effector regionBy similarity

Sequence similaritiesi

Belongs to the small GTPase superfamily. Rab family.Curated

Phylogenomic databases

eggNOGiCOG1100.
GeneTreeiENSGT00760000118937.
HOGENOMiHOG000233968.
HOVERGENiHBG009351.
InParanoidiO95716.
KOiK07884.
OMAiEPSSCSC.
OrthoDBiEOG7JQBPC.
PhylomeDBiO95716.
TreeFamiTF313199.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view]
PfamiPF00071. Ras. 1 hit.
[Graphical view]
PRINTSiPR00449. RASTRNSFRMNG.
SMARTiSM00175. RAB. 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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti64 – 641V → I.
Corresponds to variant rs3969860 [ dbSNP | Ensembl ].
VAR_051710

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
EntryMethodResolution (Å)ChainPositionsPDBsum
2GF9X-ray1.53A20-189[»]
ProteinModelPortaliO95716.
SMRiO95716. Positions 20-189.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114919. 12 interactions.
IntActiO95716. 3 interactions.
STRINGi9606.ENSP00000222120.

PTM databases

PhosphoSiteiO95716.

Proteomic databases

MaxQBiO95716.
PaxDbiO95716.
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.
GeneCardsiGC19M011435.
HGNCiHGNC:9779. RAB3D.
HPAiCAB018067.
HPA051912.
MIMi604350. gene.
neXtProtiNX_O95716.
PharmGKBiPA34134.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG1100.
GeneTreeiENSGT00760000118937.
HOGENOMiHOG000233968.
HOVERGENiHBG009351.
InParanoidiO95716.
KOiK07884.
OMAiEPSSCSC.
OrthoDBiEOG7JQBPC.
PhylomeDBiO95716.
TreeFamiTF313199.

Miscellaneous databases

EvolutionaryTraceiO95716.
GeneWikiiRAB3D.
GenomeRNAii9545.
NextBioi35795.
PROiO95716.
SOURCEiSearch...

Gene expression databases

BgeeiO95716.
CleanExiHS_RAB3D.
ExpressionAtlasiO95716. baseline and differential.
GenevestigatoriO95716.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view]
PfamiPF00071. Ras. 1 hit.
[Graphical view]
PRINTSiPR00449. RASTRNSFRMNG.
SMARTiSM00175. RAB. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51419. RAB. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning of cDNA encoding human Rab3D whose expression is upregulated with myeloid differentiation."
    Nishio H., Suda T., Sawada K., Miyamoto T., Koike T., Yamaguchi Y.
    Biochim. Biophys. Acta 1444:283-290(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Hematopoietic.
  2. "cDNA clones of human proteins involved in signal transduction sequenced by the Guthrie cDNA resource center (www.cdna.org)."
    Puhl H.L. III, Ikeda S.R., Aronstam R.S.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Ovary.
  4. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  5. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
  6. "Crystal structure of human RAB3D in complex with GDP."
    Structural genomics consortium (SGC)
    Submitted (JAN-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.53 ANGSTROMS) OF 20-189 IN COMPLEX WITH GDP.

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: March 4, 2015
This is version 142 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

External Data

Dasty 3

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 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.