RAB3B_HUMAN
ID RAB3B_HUMAN Reviewed; 219 AA.
AC P20337; Q5VUL2; Q9BSI1;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 31-OCT-2003, sequence version 2.
DT 03-AUG-2022, entry version 203.
DE RecName: Full=Ras-related protein Rab-3B;
GN Name=RAB3B;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=2501306; DOI=10.1016/s0021-9258(18)63872-4;
RA Zahraoui A., Touchot N., Chardin P., Tavitian A.;
RT "The human Rab genes encode a family of GTP-binding proteins related to
RT yeast YPT1 and SEC4 products involved in secretion.";
RL J. Biol. Chem. 264:12394-12401(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain;
RA Puhl H.L. III, Ikeda S.R., Aronstam R.S.;
RT "cDNA clones of human proteins involved in signal transduction sequenced by
RT the Guthrie cDNA resource center (www.cdna.org).";
RL Submitted (APR-2002) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16710414; DOI=10.1038/nature04727;
RA Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A.,
RA Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C.,
RA Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.,
RA Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C.,
RA Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W.,
RA Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J.,
RA Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J.,
RA Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y.,
RA Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J.,
RA Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
RA Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
RA Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
RA Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S.,
RA Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K.,
RA Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R.,
RA Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M.,
RA Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S.,
RA Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J.,
RA Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W.,
RA McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
RA Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
RA Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
RA Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
RA Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S.,
RA Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M.,
RA White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H.,
RA Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E.,
RA Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G.,
RA Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.;
RT "The DNA sequence and biological annotation of human chromosome 1.";
RL Nature 441:315-321(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Lung;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-190, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T.,
RA Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.;
RT "System-wide temporal characterization of the proteome and phosphoproteome
RT of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
RN [6]
RP INTERACTION WITH GDI2; CHM AND CHML, PHOSPHORYLATION AT THR-86, AND
RP MUTAGENESIS OF THR-86.
RX PubMed=29125462; DOI=10.7554/elife.31012;
RA Steger M., Diez F., Dhekne H.S., Lis P., Nirujogi R.S., Karayel O.,
RA Tonelli F., Martinez T.N., Lorentzen E., Pfeffer S.R., Alessi D.R.,
RA Mann M.;
RT "Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation
RT establishes a connection to ciliogenesis.";
RL Elife 6:0-0(2017).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 18-190 IN COMPLEX WITH GDP.
RG Structural genomics consortium (SGC);
RT "Crystal structure of human RAB3B GTPase bound with GDP.";
RL Submitted (FEB-2009) to the PDB data bank.
CC -!- FUNCTION: Protein transport. Probably involved in vesicular traffic (By
CC similarity). {ECO:0000250}.
CC -!- SUBUNIT: Interacts with RIMS1, RIMS2, RPH3A and RPH3AL. The GTP-bound
CC form interacts with GAS8/DRC4 (via coiled-coil domains) (By
CC similarity). Interacts with GDI2, CHM and CHML; phosphorylation at Thr-
CC 86 disrupts these interactions (PubMed:29125462). Interacts with MADD
CC (via uDENN domain); the GTP-bound form is preferred for interaction (By
CC similarity). {ECO:0000250|UniProtKB:Q9CZT8,
CC ECO:0000269|PubMed:29125462}.
CC -!- INTERACTION:
CC P20337; P47224: RABIF; NbExp=5; IntAct=EBI-12894629, EBI-713992;
CC P20337; Q9H8Y1: VRTN; NbExp=3; IntAct=EBI-12894629, EBI-12894399;
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Lipid-anchor
CC {ECO:0000305}; Cytoplasmic side {ECO:0000305}. Golgi apparatus
CC {ECO:0000250|UniProtKB:Q9CZT8}. Note=Colocalizes with GAS8/DRC4 in the
CC Golgi apparatus. {ECO:0000250|UniProtKB:Q9CZT8}.
CC -!- PTM: Phosphorylation of Thr-86 in the switch II region by LRRK2
CC prevents the association of RAB regulatory proteins, including CHM,
CC CHML and RAB GDP dissociation inhibitor GDI2.
CC {ECO:0000269|PubMed:29125462}.
CC -!- SIMILARITY: Belongs to the small GTPase superfamily. Rab family.
CC {ECO:0000305}.
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DR EMBL; M28214; AAA60243.1; -; mRNA.
DR EMBL; AF498932; AAM21080.1; -; mRNA.
DR EMBL; AL589663; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AL445685; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC005035; AAH05035.1; -; mRNA.
DR CCDS; CCDS560.1; -.
DR PIR; D34323; D34323.
DR RefSeq; NP_002858.2; NM_002867.3.
DR RefSeq; XP_016857447.1; XM_017001958.1.
DR PDB; 3DZ8; X-ray; 1.90 A; A=18-190.
DR PDBsum; 3DZ8; -.
DR AlphaFoldDB; P20337; -.
DR SMR; P20337; -.
DR BioGRID; 111803; 358.
DR IntAct; P20337; 18.
DR MINT; P20337; -.
DR STRING; 9606.ENSP00000360718; -.
DR iPTMnet; P20337; -.
DR MetOSite; P20337; -.
DR PhosphoSitePlus; P20337; -.
DR SwissPalm; P20337; -.
DR BioMuta; RAB3B; -.
DR DMDM; 38258903; -.
DR EPD; P20337; -.
DR jPOST; P20337; -.
DR MassIVE; P20337; -.
DR MaxQB; P20337; -.
DR PaxDb; P20337; -.
DR PeptideAtlas; P20337; -.
DR PRIDE; P20337; -.
DR ProteomicsDB; 53749; -.
DR Antibodypedia; 19062; 177 antibodies from 26 providers.
DR DNASU; 5865; -.
DR Ensembl; ENST00000371655.4; ENSP00000360718.3; ENSG00000169213.7.
DR GeneID; 5865; -.
DR KEGG; hsa:5865; -.
DR MANE-Select; ENST00000371655.4; ENSP00000360718.3; NM_002867.4; NP_002858.2.
DR UCSC; uc001cth.3; human.
DR CTD; 5865; -.
DR DisGeNET; 5865; -.
DR GeneCards; RAB3B; -.
DR HGNC; HGNC:9778; RAB3B.
DR HPA; ENSG00000169213; Group enriched (brain, pituitary gland, prostate).
DR MIM; 179510; gene.
DR neXtProt; NX_P20337; -.
DR OpenTargets; ENSG00000169213; -.
DR PharmGKB; PA34133; -.
DR VEuPathDB; HostDB:ENSG00000169213; -.
DR eggNOG; KOG0093; Eukaryota.
DR GeneTree; ENSGT00940000159943; -.
DR HOGENOM; CLU_041217_10_1_1; -.
DR InParanoid; P20337; -.
DR OMA; AICEKMS; -.
DR OrthoDB; 1426655at2759; -.
DR PhylomeDB; P20337; -.
DR TreeFam; TF313199; -.
DR PathwayCommons; P20337; -.
DR Reactome; R-HSA-8873719; RAB geranylgeranylation.
DR SignaLink; P20337; -.
DR BioGRID-ORCS; 5865; 9 hits in 1076 CRISPR screens.
DR ChiTaRS; RAB3B; human.
DR EvolutionaryTrace; P20337; -.
DR GeneWiki; RAB3B; -.
DR GenomeRNAi; 5865; -.
DR Pharos; P20337; Tbio.
DR PRO; PR:P20337; -.
DR Proteomes; UP000005640; Chromosome 1.
DR RNAct; P20337; protein.
DR Bgee; ENSG00000169213; Expressed in islet of Langerhans and 102 other tissues.
DR Genevisible; P20337; HS.
DR GO; GO:0098993; C:anchored component of synaptic vesicle membrane; IDA:SynGO.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IEA:Ensembl.
DR GO; GO:0098691; C:dopaminergic synapse; IDA:SynGO.
DR GO; GO:0005768; C:endosome; IBA:GO_Central.
DR GO; GO:0070062; C:extracellular exosome; HDA:UniProtKB.
DR GO; GO:0005794; C:Golgi apparatus; IEA:UniProtKB-SubCell.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; IBA:GO_Central.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR GO; GO:0008021; C:synaptic vesicle; IBA:GO_Central.
DR GO; GO:0031982; C:vesicle; IDA:UniProtKB.
DR GO; GO:0019003; F:GDP binding; IDA:UniProtKB.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003924; F:GTPase activity; IDA:UniProtKB.
DR GO; GO:0031489; F:myosin V binding; IPI:UniProtKB.
DR GO; GO:0019882; P:antigen processing and presentation; IMP:UniProtKB.
DR GO; GO:0051586; P:positive regulation of dopamine uptake involved in synaptic transmission; IDA:UniProtKB.
DR GO; GO:0072659; P:protein localization to plasma membrane; IBA:GO_Central.
DR GO; GO:0009306; P:protein secretion; IBA:GO_Central.
DR GO; GO:0017157; P:regulation of exocytosis; IBA:GO_Central.
DR GO; GO:0098693; P:regulation of synaptic vesicle cycle; IDA:SynGO.
DR GO; GO:0097494; P:regulation of vesicle size; IDA:UniProtKB.
DR GO; GO:0006904; P:vesicle docking involved in exocytosis; IBA:GO_Central.
DR CDD; cd01865; Rab3; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR037872; Rab3.
DR InterPro; IPR005225; Small_GTP-bd_dom.
DR InterPro; IPR001806; Small_GTPase.
DR Pfam; PF00071; Ras; 1.
DR SMART; SM00174; RHO; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00231; small_GTP; 1.
DR PROSITE; PS51419; RAB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cell membrane; Golgi apparatus; GTP-binding;
KW Lipoprotein; Membrane; Methylation; Nucleotide-binding; Phosphoprotein;
KW Prenylation; Protein transport; Reference proteome; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:O95716"
FT CHAIN 2..219
FT /note="Ras-related protein Rab-3B"
FT /id="PRO_0000121081"
FT MOTIF 51..59
FT /note="Effector region"
FT /evidence="ECO:0000250"
FT BINDING 29..37
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0007744|PDB:3DZ8"
FT BINDING 48..54
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:P63012"
FT BINDING 77..81
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:P62820"
FT BINDING 135..138
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0007744|PDB:3DZ8"
FT BINDING 165..167
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0007744|PDB:3DZ8"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0000250|UniProtKB:O95716"
FT MOD_RES 86
FT /note="Phosphothreonine; by LRRK2"
FT /evidence="ECO:0000269|PubMed:29125462"
FT MOD_RES 188
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q63941"
FT MOD_RES 190
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21406692"
FT MOD_RES 219
FT /note="Cysteine methyl ester"
FT /evidence="ECO:0000250"
FT LIPID 217
FT /note="S-geranylgeranyl cysteine"
FT /evidence="ECO:0000250"
FT LIPID 219
FT /note="S-geranylgeranyl cysteine"
FT /evidence="ECO:0000250"
FT MUTAGEN 86
FT /note="T->A: Loss of phosphorylation. No effect on GDI2,
FT CHM and CHML binding."
FT /evidence="ECO:0000269|PubMed:29125462"
FT MUTAGEN 86
FT /note="T->E: Phosphomimetic mutant. Loss of GDI2, CHM and
FT CHML binding."
FT /evidence="ECO:0000269|PubMed:29125462"
FT CONFLICT 9
FT /note="T -> H (in Ref. 1; AAA60243)"
FT /evidence="ECO:0000305"
FT CONFLICT 40
FT /note="F -> L (in Ref. 1; AAA60243)"
FT /evidence="ECO:0000305"
FT STRAND 18..21
FT /evidence="ECO:0007829|PDB:3DZ8"
FT STRAND 23..30
FT /evidence="ECO:0007829|PDB:3DZ8"
FT HELIX 35..45
FT /evidence="ECO:0007829|PDB:3DZ8"
FT STRAND 51..55
FT /evidence="ECO:0007829|PDB:3DZ8"
FT TURN 56..58
FT /evidence="ECO:0007829|PDB:3DZ8"
FT STRAND 59..66
FT /evidence="ECO:0007829|PDB:3DZ8"
FT TURN 67..70
FT /evidence="ECO:0007829|PDB:3DZ8"
FT STRAND 71..76
FT /evidence="ECO:0007829|PDB:3DZ8"
FT HELIX 78..83
FT /evidence="ECO:0007829|PDB:3DZ8"
FT HELIX 85..92
FT /evidence="ECO:0007829|PDB:3DZ8"
FT STRAND 97..103
FT /evidence="ECO:0007829|PDB:3DZ8"
FT HELIX 107..111
FT /evidence="ECO:0007829|PDB:3DZ8"
FT HELIX 113..123
FT /evidence="ECO:0007829|PDB:3DZ8"
FT STRAND 129..135
FT /evidence="ECO:0007829|PDB:3DZ8"
FT HELIX 140..142
FT /evidence="ECO:0007829|PDB:3DZ8"
FT HELIX 147..157
FT /evidence="ECO:0007829|PDB:3DZ8"
FT STRAND 160..163
FT /evidence="ECO:0007829|PDB:3DZ8"
FT TURN 166..169
FT /evidence="ECO:0007829|PDB:3DZ8"
FT HELIX 172..186
FT /evidence="ECO:0007829|PDB:3DZ8"
SQ SEQUENCE 219 AA; 24758 MW; B73A014B4295A60D CRC64;
MASVTDGKTG VKDASDQNFD YMFKLLIIGN SSVGKTSFLF RYADDTFTPA FVSTVGIDFK
VKTVYRHEKR VKLQIWDTAG QERYRTITTA YYRGAMGFIL MYDITNEESF NAVQDWATQI
KTYSWDNAQV ILVGNKCDME EERVVPTEKG QLLAEQLGFD FFEASAKENI SVRQAFERLV
DAICDKMSDS LDTDPSMLGS SKNTRLSDTP PLLQQNCSC
