P61020 (RAB5B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ras-related protein Rab-5B

Gene names

Name:

RAB5B

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	215 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Protein transport. Probably involved in vesicular traffic By similarity.
Enzyme regulation	Regulated by guanine nucleotide exchange factors (GEFs) which promote the exchange of bound GDP for free GTP.
Subunit structure	Binds EEA1. Interacts with RIN2 and RIN3, which probably regulate its pathway, possibly by acting as GEFs. Ref.8 Ref.9
Subcellular location	Cell membrane; Lipid-anchor; Cytoplasmic side. Early endosome membrane; Lipid-anchor. Melanosome. Note: Enriched in stage I melanosomes. Ref.10
Sequence similarities	Belongs to the small GTPase superfamily. Rab family.
Sequence caution	The sequence AAH40143.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Protein transport Transport
Cellular component	Cell membrane Endosome Membrane
Coding sequence diversity	Alternative splicing
Ligand	GTP-binding Nucleotide-binding
PTM	Lipoprotein Prenylation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	endosome organization Inferred from electronic annotation. Source: Compara protein transport Inferred from electronic annotation. Source: UniProtKB-KW regulation of endocytosis Inferred from electronic annotation. Source: Compara small GTPase mediated signal transduction Inferred from electronic annotation. Source: InterPro
Cellular_component	early endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell endocytic vesicle Inferred from electronic annotation. Source: Compara endosome Inferred from direct assay Ref.8. Source: UniProtKB melanosome Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Traceable author statement Ref.1. Source: ProtInc
Molecular_function	GDP binding Inferred from direct assay PubMed 20937701. Source: UniProtKB GTP binding Inferred from electronic annotation. Source: UniProtKB-KW GTP-dependent protein binding Inferred from direct assay Ref.8. Source: UniProtKB GTPase activity Traceable author statement Ref.1. Source: ProtInc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
EEA1	Q15075	3	EBI-399401,EBI-298113

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: P61020-1)

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.

Isoform 2 (identifier: P61020-2)

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

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 215

215

Ras-related protein Rab-5B

PRO_0000121107

Regions

Nucleotide binding

27 – 35

9

GTP

Nucleotide binding

75 – 79

5

GTP By similarity

Nucleotide binding

133 – 136

4

GTP

Nucleotide binding

163 – 165

3

GTP

Motif

49 – 57

9

Effector region Potential

Amino acid modifications

Lipidation

212

1

S-geranylgeranyl cysteine By similarity

Lipidation

213

1

S-geranylgeranyl cysteine By similarity

Natural variations

Alternative sequence

106 – 146

41

Missing in isoform 2.

VSP_045301

Experimental info

Mutagenesis

34

1

S → N: Constitutively inactivated. Strongly reduces interaction with RIN2. Ref.9

Mutagenesis

79

1

Q → L: Constitutively active. Ref.9

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

215

Helix Strand Turn

Details...

Beta strand

19 – 26

8

Helix

33 – 42

10

Beta strand

54 – 56

3

Beta strand

58 – 62

5

Beta strand

69 – 74

6

Helix

83 – 85

3

Helix

86 – 90

5

Beta strand

95 – 101

7

Helix

105 – 121

17

Beta strand

127 – 133

7

Helix

135 – 140

6

Helix

145 – 154

10

Beta strand

158 – 161

4

Turn

164 – 166

3

Helix

170 – 180

11

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified April 26, 2004. Version 1. Checksum: D47AD834BCF8B591	FASTA	215	23,707
	10 20 30 40 50 60 MTSRSTARPN GQPQASKICQ FKLVLLGESA VGKSSLVLRF VKGQFHEYQE STIGAAFLTQ 70 80 90 100 110 120 SVCLDDTTVK FEIWDTAGQE RYHSLAPMYY RGAQAAIVVY DITNQETFAR AKTWVKELQR 130 140 150 160 170 180 QASPSIVIAL AGNKADLANK RMVEYEEAQA YADDNSLLFM ETSAKTAMNV NDLFLAIAKK 190 200 210 LPKSEPQNLG GAAGRSRGVD LHEQSQQNKS QCCSN
	Isoform 2 [UniParc]. Checksum: 90D1C43B99761B6E	FASTA	174	19,090
	10 20 30 40 50 60 MTSRSTARPN GQPQASKICQ FKLVLLGESA VGKSSLVLRF VKGQFHEYQE STIGAAFLTQ 70 80 90 100 110 120 SVCLDDTTVK FEIWDTAGQE RYHSLAPMYY RGAQAAIVVY DITNQEAQAY ADDNSLLFME 130 140 150 160 170 TSAKTAMNVN DLFLAIAKKL PKSEPQNLGG AAGRSRGVDL HEQSQQNKSQ CCSN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification and subcellular localization of human rab5b, a new member of the ras-related superfamily of GTPases." Wilson D.B., Wilson M.P. J. Clin. Invest. 89:996-1005(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[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 (APR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Brain.
[3]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Tissue: Testis and Thalamus.
[4]	"The full-ORF clone resource of the German cDNA consortium." Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I. BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Endometrium.
[5]	"The finished DNA sequence of human chromosome 12." Scherer S.E., Muzny D.M., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J., Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R. , Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Montgomery K.T., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Lovering R.C., Wheeler D.A., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clerc-Blankenburg K.P., Davis C., Delgado O., Dinh H.H., Draper H., Gonzalez-Garay M.L., Havlak P., Jackson L.R., Jacob L.S., Kelly S.H., Li L., Li Z., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Pasternak S., Perez L.M., Plopper F.J.H., Santibanez J., Shen H., Tabor P.E., Verduzco D., Waldron L., Wang Q., Williams G.A., Zhang J., Zhou J., Allen C.C., Amin A.G., Anyalebechi V., Bailey M., Barbaria J.A., Bimage K.E., Bryant N.P., Burch P.E., Burkett C.E., Burrell K.L., Calderon E., Cardenas V., Carter K., Casias K., Cavazos I., Cavazos S.R., Ceasar H., Chacko J., Chan S.N., Chavez D., Christopoulos C., Chu J., Cockrell R., Cox C.D., Dang M., Dathorne S.R., David R., Davis C.M., Davy-Carroll L., Deshazo D.R., Donlin J.E., D'Souza L., Eaves K.A., Egan A., Emery-Cohen A.J., Escotto M., Flagg N., Forbes L.D., Gabisi A.M., Garza M., Hamilton C., Henderson N., Hernandez O., Hines S., Hogues M.E., Huang M., Idlebird D.G., Johnson R., Jolivet A., Jones S., Kagan R., King L.M., Leal B., Lebow H., Lee S., LeVan J.M., Lewis L.C., London P., Lorensuhewa L.M., Loulseged H., Lovett D.A., Lucier A., Lucier R.L., Ma J., Madu R.C., Mapua P., Martindale A.D., Martinez E., Massey E., Mawhiney S., Meador M.G., Mendez S., Mercado C., Mercado I.C., Merritt C.E., Miner Z.L., Minja E., Mitchell T., Mohabbat F., Mohabbat K., Montgomery B., Moore N., Morris S., Munidasa M., Ngo R.N., Nguyen N.B., Nickerson E., Nwaokelemeh O.O., Nwokenkwo S., Obregon M., Oguh M., Oragunye N., Oviedo R.J., Parish B.J., Parker D.N., Parrish J., Parks K.L., Paul H.A., Payton B.A., Perez A., Perrin W., Pickens A., Primus E.L., Pu L.-L., Puazo M., Quiles M.M., Quiroz J.B., Rabata D., Reeves K., Ruiz S.J., Shao H., Sisson I., Sonaike T., Sorelle R.P., Sutton A.E., Svatek A.F., Svetz L.A., Tamerisa K.S., Taylor T.R., Teague B., Thomas N., Thorn R.D., Trejos Z.Y., Trevino B.K., Ukegbu O.N., Urban J.B., Vasquez L.I., Vera V.A., Villasana D.M., Wang L., Ward-Moore S., Warren J.T., Wei X., White F., Williamson A.L., Wleczyk R., Wooden H.S., Wooden S.H., Yen J., Yoon L., Yoon V., Zorrilla S.E., Nelson D., Kucherlapati R., Weinstock G., Gibbs R.A. Nature 440:346-351(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]	"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(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Eye, PNS and Skin.
[8]	"Direct interaction of EEA1 with Rab5b." Callaghan J.M., Nixon S., Bucci C., Toh B.-H., Stenmark H. Eur. J. Biochem. 265:361-366(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH EEA1.
[9]	"A novel binding protein composed of homophilic tetramer exhibits unique properties for the small GTPase Rab5." Saito K., Murai J., Kajiho H., Kontani K., Kurosu H., Katada T. J. Biol. Chem. 277:3412-3418(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RIN2 AND RIN3, MUTAGENESIS OF SER-34 AND GLN-79.
[10]	"Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes." Chi A., Valencia J.C., Hu Z.-Z., Watabe H., Yamaguchi H., Mangini N.J., Huang H., Canfield V.A., Cheng K.C., Yang F., Abe R., Yamagishi S., Shabanowitz J., Hearing V.J., Wu C., Appella E., Hunt D.F. J. Proteome Res. 5:3135-3144(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY. Tissue: Melanoma.
[11]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]	"Crystal structure of human RAB5B in complex with GDP." Structural genomics consortium (SGC) Submitted (FEB-2009) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 15-191 IN COMPLEX WITH GDP.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00017344.

PIR

A43925.

RefSeq

NP_001238965.1. NM_001252036.1.
NP_001238966.1. NM_001252037.1.
NP_002859.1. NM_002868.3.

UniGene

Hs.157659.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2HEI	X-ray	1.55	A/B	15-191	[»]

ProteinModelPortal

P61020.

ModBase

Search...

Protein-protein interaction databases

IntAct

P61020. 6 interactions.

STRING

9606.ENSP00000353444.

PTM databases

PhosphoSite

P61020.

Polymorphism databases

DMDM

46577637.

Proteomic databases

PaxDb

P61020.

PRIDE

P61020.

Protocols and materials databases

DNASU

5869.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000360299; ENSP00000353444; ENSG00000111540.
ENST00000448789; ENSP00000391319; ENSG00000111540.
ENST00000553116; ENSP00000450168; ENSG00000111540.

GeneID

5869.

KEGG

hsa:5869.

UCSC

uc001siv.3. human.

Organism-specific databases

CTD

5869.

GeneCards

GC12P056368.

HGNC

HGNC:9784. RAB5B.

HPA

CAB010224.

MIM

179514. gene.

neXtProt

NX_P61020.

PharmGKB

PA34144.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1100.

HOVERGEN

HBG009351.

InParanoid

P61020.

KO

K07888.

OMA

GTQGKIC.

OrthoDB

EOG4Z0B6M.

PhylomeDB

P61020.

Gene expression databases

ArrayExpress

P61020.

Bgee

P61020.

CleanEx

HS_RAB5B.

Genevestigator

P61020.

Family and domain databases

InterPro

IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view]

Pfam

PF00071. Ras. 1 hit.
[Graphical view]

PRINTS

PR00449. RASTRNSFRMNG.

SMART

SM00175. RAB. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00231. small_GTP. 1 hit.

PROSITE

PS51419. RAB. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

RAB5B. human.

EvolutionaryTrace

P61020.

GenomeRNAi

5869.

NextBio

22794.

SOURCE

Search...

Entry information

Entry name

RAB5B_HUMAN

Accession

Primary (citable) accession number: P61020
Secondary accession number(s): A8K982 , B4DKD7, P35239, P35277, Q6PIK9, Q86TH0, Q8IXL2

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 26, 2004
Last sequence update:	April 26, 2004
Last modified:	May 1, 2013
This is version 101 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.