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Protein

Ras-related protein Rab-5B

Gene

RAB5B

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 vesicular traffic (By similarity).By similarity

Enzyme regulationi

Regulated by guanine nucleotide exchange factors (GEFs) which promote the exchange of bound GDP for free GTP.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi27 – 35GTPCombined sources1 Publication9
Nucleotide bindingi46 – 52GTPCombined sources1 Publication7
Nucleotide bindingi75 – 79GTPBy similarity5
Nucleotide bindingi133 – 136GTPCombined sources1 Publication4
Nucleotide bindingi163 – 165GTPCombined sources1 Publication3

GO - Molecular functioni

  • GDP binding Source: UniProtKB
  • GTPase activity Source: UniProtKB
  • GTP binding Source: UniProtKB-KW
  • GTP-dependent protein binding Source: UniProtKB

GO - Biological processi

  • antigen processing and presentation Source: UniProtKB
  • endosome organization Source: Ensembl
  • plasma membrane to endosome transport Source: UniProtKB
  • protein transport Source: UniProtKB-KW
  • regulation of endocytosis Source: GO_Central
  • small GTPase mediated signal transduction Source: InterPro
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000111540-MONOMER.
ReactomeiR-HSA-6798695. Neutrophil degranulation.
R-HSA-8856828. Clathrin-mediated endocytosis.
R-HSA-8876198. RAB GEFs exchange GTP for GDP on RABs.
SIGNORiP61020.

Names & Taxonomyi

Protein namesi
Recommended name:
Ras-related protein Rab-5B
Gene namesi
Name:RAB5B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:9784. RAB5B.

Subcellular locationi

GO - Cellular componenti

  • early endosome Source: GO_Central
  • early endosome membrane Source: UniProtKB-SubCell
  • endocytic vesicle Source: GO_Central
  • endosome Source: UniProtKB
  • extracellular exosome Source: UniProtKB
  • intracellular Source: LIFEdb
  • melanosome Source: UniProtKB-SubCell
  • membrane Source: ProtInc
  • plasma membrane Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Endosome, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi34S → N: Constitutively inactivated. Strongly reduces interaction with RIN2. 1 Publication1
Mutagenesisi79Q → L: Constitutively active. 1 Publication1

Organism-specific databases

DisGeNETi5869.
OpenTargetsiENSG00000111540.
PharmGKBiPA34144.

Polymorphism and mutation databases

BioMutaiRAB5B.
DMDMi46577637.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001211072 – 215Ras-related protein Rab-5BAdd BLAST214

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylthreonineCombined sources1
Lipidationi212S-geranylgeranyl cysteineBy similarity1
Lipidationi213S-geranylgeranyl cysteineBy similarity1

Keywords - PTMi

Acetylation, Lipoprotein, Prenylation

Proteomic databases

EPDiP61020.
MaxQBiP61020.
PaxDbiP61020.
PeptideAtlasiP61020.
PRIDEiP61020.

PTM databases

iPTMnetiP61020.
PhosphoSitePlusiP61020.
SwissPalmiP61020.

Expressioni

Gene expression databases

BgeeiENSG00000111540.
CleanExiHS_RAB5B.
ExpressionAtlasiP61020. baseline and differential.
GenevisibleiP61020. HS.

Organism-specific databases

HPAiCAB010224.
HPA060685.

Interactioni

Subunit structurei

Binds EEA1. Interacts with RIN2 and RIN3, which probably regulate its pathway, possibly by acting as GEFs.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
EEA1Q150753EBI-399401,EBI-298113
LRRK2Q5S0079EBI-399401,EBI-5323863

GO - Molecular functioni

  • GTP-dependent protein binding Source: UniProtKB

Protein-protein interaction databases

BioGridi111807. 57 interactors.
IntActiP61020. 14 interactors.
MINTiMINT-3022222.
STRINGi9606.ENSP00000353444.

Structurei

Secondary structure

1215
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi19 – 26Combined sources8
Helixi33 – 42Combined sources10
Beta strandi54 – 56Combined sources3
Beta strandi58 – 62Combined sources5
Beta strandi69 – 74Combined sources6
Helixi83 – 85Combined sources3
Helixi86 – 90Combined sources5
Beta strandi95 – 101Combined sources7
Helixi105 – 121Combined sources17
Beta strandi127 – 133Combined sources7
Helixi135 – 140Combined sources6
Helixi145 – 154Combined sources10
Beta strandi158 – 161Combined sources4
Turni164 – 166Combined sources3
Helixi170 – 180Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HEIX-ray1.55A/B15-191[»]
ProteinModelPortaliP61020.
SMRiP61020.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP61020.

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi49 – 57Effector regionSequence analysis9

Sequence similaritiesi

Belongs to the small GTPase superfamily. Rab family.Curated

Phylogenomic databases

eggNOGiKOG0092. Eukaryota.
ENOG410YCCP. LUCA.
GeneTreeiENSGT00760000119101.
HOGENOMiHOG000233968.
HOVERGENiHBG009351.
InParanoidiP61020.
KOiK07888.
OMAiKSWIREL.
OrthoDBiEOG091G0HKN.
PhylomeDBiP61020.
TreeFamiTF300199.

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]

Sequences (2)i

Sequence statusi: Complete.

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

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

Isoform 1 (identifier: P61020-1) [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
MTSRSTARPN GQPQASKICQ FKLVLLGESA VGKSSLVLRF VKGQFHEYQE
60 70 80 90 100
STIGAAFLTQ SVCLDDTTVK FEIWDTAGQE RYHSLAPMYY RGAQAAIVVY
110 120 130 140 150
DITNQETFAR AKTWVKELQR QASPSIVIAL AGNKADLANK RMVEYEEAQA
160 170 180 190 200
YADDNSLLFM ETSAKTAMNV NDLFLAIAKK LPKSEPQNLG GAAGRSRGVD
210
LHEQSQQNKS QCCSN
Length:215
Mass (Da):23,707
Last modified:April 26, 2004 - v1
Checksum:iD47AD834BCF8B591
GO
Isoform 2 (identifier: P61020-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     106-146: Missing.

Show »
Length:174
Mass (Da):19,090
Checksum:i90D1C43B99761B6E
GO

Sequence cautioni

The sequence AAH40143 differs from that shown. Reason: Erroneous initiation.Curated

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_045301106 – 146Missing in isoform 2. 1 PublicationAdd BLAST41

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54871 mRNA. Translation: CAA38653.1.
AF498937 mRNA. Translation: AAM21085.1.
AK292597 mRNA. Translation: BAF85286.1.
AK296517 mRNA. Translation: BAG59149.1.
BX537408 mRNA. Translation: CAD97650.1.
AC034102 Genomic DNA. No translation available.
CH471054 Genomic DNA. Translation: EAW96862.1.
CH471054 Genomic DNA. Translation: EAW96864.1.
BC032740 mRNA. Translation: AAH32740.1.
BC040143 mRNA. Translation: AAH40143.1. Different initiation.
BC050558 mRNA. Translation: AAH50558.2.
BC056422 mRNA. Translation: AAH56422.2.
BC065298 mRNA. Translation: AAH65298.2.
CCDSiCCDS58244.1. [P61020-2]
CCDS8900.1. [P61020-1]
PIRiA43925.
RefSeqiNP_001238965.1. NM_001252036.1. [P61020-1]
NP_001238966.1. NM_001252037.1. [P61020-2]
NP_002859.1. NM_002868.3. [P61020-1]
XP_005269108.1. XM_005269051.2. [P61020-1]
XP_005269109.1. XM_005269052.2. [P61020-1]
UniGeneiHs.157659.

Genome annotation databases

EnsembliENST00000360299; ENSP00000353444; ENSG00000111540. [P61020-1]
ENST00000448789; ENSP00000391319; ENSG00000111540. [P61020-2]
ENST00000553116; ENSP00000450168; ENSG00000111540. [P61020-1]
GeneIDi5869.
KEGGihsa:5869.
UCSCiuc001siv.4. human. [P61020-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54871 mRNA. Translation: CAA38653.1.
AF498937 mRNA. Translation: AAM21085.1.
AK292597 mRNA. Translation: BAF85286.1.
AK296517 mRNA. Translation: BAG59149.1.
BX537408 mRNA. Translation: CAD97650.1.
AC034102 Genomic DNA. No translation available.
CH471054 Genomic DNA. Translation: EAW96862.1.
CH471054 Genomic DNA. Translation: EAW96864.1.
BC032740 mRNA. Translation: AAH32740.1.
BC040143 mRNA. Translation: AAH40143.1. Different initiation.
BC050558 mRNA. Translation: AAH50558.2.
BC056422 mRNA. Translation: AAH56422.2.
BC065298 mRNA. Translation: AAH65298.2.
CCDSiCCDS58244.1. [P61020-2]
CCDS8900.1. [P61020-1]
PIRiA43925.
RefSeqiNP_001238965.1. NM_001252036.1. [P61020-1]
NP_001238966.1. NM_001252037.1. [P61020-2]
NP_002859.1. NM_002868.3. [P61020-1]
XP_005269108.1. XM_005269051.2. [P61020-1]
XP_005269109.1. XM_005269052.2. [P61020-1]
UniGeneiHs.157659.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HEIX-ray1.55A/B15-191[»]
ProteinModelPortaliP61020.
SMRiP61020.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111807. 57 interactors.
IntActiP61020. 14 interactors.
MINTiMINT-3022222.
STRINGi9606.ENSP00000353444.

PTM databases

iPTMnetiP61020.
PhosphoSitePlusiP61020.
SwissPalmiP61020.

Polymorphism and mutation databases

BioMutaiRAB5B.
DMDMi46577637.

Proteomic databases

EPDiP61020.
MaxQBiP61020.
PaxDbiP61020.
PeptideAtlasiP61020.
PRIDEiP61020.

Protocols and materials databases

DNASUi5869.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000360299; ENSP00000353444; ENSG00000111540. [P61020-1]
ENST00000448789; ENSP00000391319; ENSG00000111540. [P61020-2]
ENST00000553116; ENSP00000450168; ENSG00000111540. [P61020-1]
GeneIDi5869.
KEGGihsa:5869.
UCSCiuc001siv.4. human. [P61020-1]

Organism-specific databases

CTDi5869.
DisGeNETi5869.
GeneCardsiRAB5B.
HGNCiHGNC:9784. RAB5B.
HPAiCAB010224.
HPA060685.
MIMi179514. gene.
neXtProtiNX_P61020.
OpenTargetsiENSG00000111540.
PharmGKBiPA34144.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0092. Eukaryota.
ENOG410YCCP. LUCA.
GeneTreeiENSGT00760000119101.
HOGENOMiHOG000233968.
HOVERGENiHBG009351.
InParanoidiP61020.
KOiK07888.
OMAiKSWIREL.
OrthoDBiEOG091G0HKN.
PhylomeDBiP61020.
TreeFamiTF300199.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000111540-MONOMER.
ReactomeiR-HSA-6798695. Neutrophil degranulation.
R-HSA-8856828. Clathrin-mediated endocytosis.
R-HSA-8876198. RAB GEFs exchange GTP for GDP on RABs.
SIGNORiP61020.

Miscellaneous databases

ChiTaRSiRAB5B. human.
EvolutionaryTraceiP61020.
GeneWikiiRAB5B.
GenomeRNAii5869.
PROiP61020.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000111540.
CleanExiHS_RAB5B.
ExpressionAtlasiP61020. baseline and differential.
GenevisibleiP61020. 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 nameiRAB5B_HUMAN
AccessioniPrimary (citable) accession number: P61020
Secondary accession number(s): A8K982
, B4DKD7, P35239, P35277, Q6PIK9, Q86TH0, Q8IXL2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: April 26, 2004
Last modified: November 30, 2016
This is version 137 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 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.