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Q9SN68

- RAF2B_ARATH

UniProt

Q9SN68 - RAF2B_ARATH

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Protein
Ras-related protein RABF2b
Gene
RABF2B, ARA-7, RAB5B, At4g19640, F24J7.190
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Endosomal protein that may be involved in endocytosis.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi17 – 248GTP
Nucleotide bindingi65 – 695GTP By similarity
Nucleotide bindingi123 – 1264GTP
Nucleotide bindingi153 – 1542GTP

GO - Molecular functioni

  1. GTP binding Source: UniProtKB
  2. protein binding Source: UniProtKB

GO - Biological processi

  1. endocytosis Source: UniProtKB-KW
  2. protein transport Source: InterPro
  3. small GTPase mediated signal transduction Source: InterPro
Complete GO annotation...

Keywords - Biological processi

Endocytosis

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Ras-related protein RABF2b
Short name:
AtRABF2b
Alternative name(s):
Ras-related protein Ara-7
Ras-related protein Rab5B
Short name:
AtRab5B
Gene namesi
Name:RABF2B
Synonyms:ARA-7, RAB5B
Ordered Locus Names:At4g19640
ORF Names:F24J7.190
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 4

Organism-specific databases

TAIRiAT4G19640.

Subcellular locationi

Early endosome membrane. Endosome membrane. Vacuole membrane. Cell membrane; Lipid-anchor Inferred
Note: Prevacuolar compartment.5 Publications

GO - Cellular componenti

  1. early endosome Source: UniProtKB
  2. early endosome membrane Source: UniProtKB-SubCell
  3. endoplasmic reticulum Source: TAIR
  4. endosome Source: TAIR
  5. plasma membrane Source: TAIR
  6. vacuolar membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Endosome, Membrane, Vacuole

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi19 – 191V → T: Loss of interaction with VPS9A. 1 Publication
Mutagenesisi24 – 241S → N: Dominant negative (GDP-bound form); no effect on the interaction with VPS9A. 1 Publication
Mutagenesisi36 – 361V → P: No effect on the interaction with VPS9A. 1 Publication
Mutagenesisi42 – 421T → A: No effect on the interaction with VPS9A. 1 Publication
Mutagenesisi44 – 441G → P: No effect on the interaction with VPS9A. 1 Publication
Mutagenesisi46 – 461A → D: Loss of interaction with VPS9A. 1 Publication
Mutagenesisi47 – 471F → A: Loss of interaction with VPS9A. 1 Publication
Mutagenesisi64 – 641W → A: Loss of interaction with VPS9A. 1 Publication
Mutagenesisi67 – 671A → G: Loss of interaction with VPS9A. 1 Publication
Mutagenesisi69 – 691Q → E: Loss of interaction with VPS9A. 2 Publications
Mutagenesisi69 – 691Q → L: Constitutively active (GTP-bound form); loss of targeting to plasma membrane and interaction with VPS9A. 2 Publications
Mutagenesisi74 – 741S → A: Loss of interaction with VPS9A. 1 Publication
Mutagenesisi75 – 751L → A: Loss of interaction with VPS9A. 1 Publication
Mutagenesisi78 – 781M → A: Loss of interaction with VPS9A. 1 Publication
Mutagenesisi79 – 791Y → A: Loss of interaction with VPS9A. 1 Publication
Mutagenesisi123 – 1231N → I: Blocks nucleotide binding; no effect on the interaction with VPS9A. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 200200Ras-related protein RABF2b
PRO_0000406605Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi198 – 1981S-geranylgeranyl cysteine By similarity
Lipidationi199 – 1991S-geranylgeranyl cysteine By similarity

Keywords - PTMi

Lipoprotein, Prenylation

Proteomic databases

PaxDbiQ9SN68.
PRIDEiQ9SN68.

Expressioni

Tissue specificityi

Expressed in roots and actively dividing cells.1 Publication

Inductioni

Activated by VPS9A.1 Publication

Gene expression databases

ArrayExpressiQ9SN68.
GenevestigatoriQ9SN68.

Interactioni

Subunit structurei

Interacts with VPS9A homodimer.2 Publications

Protein-protein interaction databases

BioGridi12999. 1 interaction.
IntActiQ9SN68. 2 interactions.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 168
Helixi23 – 3210
Turni36 – 383
Beta strandi41 – 433
Beta strandi46 – 549
Beta strandi57 – 659
Helixi70 – 767
Helixi77 – 804
Beta strandi84 – 918
Helixi95 – 11117
Beta strandi117 – 1237
Turni128 – 1303
Helixi135 – 14410
Beta strandi148 – 1514
Beta strandi154 – 1563
Helixi160 – 16910

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EFCX-ray2.09B/D1-179[»]
2EFDX-ray3.00B/D1-179[»]
2EFEX-ray2.08B/D1-179[»]
2EFHX-ray2.10B/D1-179[»]
4G01X-ray2.20B1-179[»]
ProteinModelPortaliQ9SN68.
SMRiQ9SN68. Positions 8-172.

Miscellaneous databases

EvolutionaryTraceiQ9SN68.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi39 – 479Effector region By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1100.
HOGENOMiHOG000233968.
InParanoidiQ9SN68.
OMAiTNVKEIF.
PhylomeDBiQ9SN68.

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.

Q9SN68-1 [UniParc]FASTAAdd to Basket

« Hide

MAAAGNKSIN AKLVLLGDVG AGKSSLVLRF VKDQFVEFQE STIGAAFFSQ    50
TLAVNDATVK FEIWDTAGQE RYHSLAPMYY RGAAAAIIVF DVTNQASFER 100
AKKWVQELQA QGNPNMVMAL AGNKSDLLDA RKVTAEDAQT YAQENGLFFM 150
ETSAKTATNV KEIFYEIARR LPRVQPTENP TGMVLPDRAM DRAVSSSCCA 200
Length:200
Mass (Da):21,873
Last modified:May 1, 2000 - v1
Checksum:i769F75CFC708C6D0
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB038491 mRNA. Translation: BAB32669.1.
AL021768 Genomic DNA. Translation: CAA16940.1.
AL161551 Genomic DNA. Translation: CAB78966.1.
CP002687 Genomic DNA. Translation: AEE84207.1.
AF370309 mRNA. Translation: AAK44124.1.
AY052670 mRNA. Translation: AAK96574.1.
AY063095 mRNA. Translation: AAL34269.1.
PIRiT06157.
RefSeqiNP_193699.1. NM_118084.4.
UniGeneiAt.2030.

Genome annotation databases

EnsemblPlantsiAT4G19640.1; AT4G19640.1; AT4G19640.
GeneIDi827706.
KEGGiath:AT4G19640.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB038491 mRNA. Translation: BAB32669.1 .
AL021768 Genomic DNA. Translation: CAA16940.1 .
AL161551 Genomic DNA. Translation: CAB78966.1 .
CP002687 Genomic DNA. Translation: AEE84207.1 .
AF370309 mRNA. Translation: AAK44124.1 .
AY052670 mRNA. Translation: AAK96574.1 .
AY063095 mRNA. Translation: AAL34269.1 .
PIRi T06157.
RefSeqi NP_193699.1. NM_118084.4.
UniGenei At.2030.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2EFC X-ray 2.09 B/D 1-179 [» ]
2EFD X-ray 3.00 B/D 1-179 [» ]
2EFE X-ray 2.08 B/D 1-179 [» ]
2EFH X-ray 2.10 B/D 1-179 [» ]
4G01 X-ray 2.20 B 1-179 [» ]
ProteinModelPortali Q9SN68.
SMRi Q9SN68. Positions 8-172.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 12999. 1 interaction.
IntActi Q9SN68. 2 interactions.

Proteomic databases

PaxDbi Q9SN68.
PRIDEi Q9SN68.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT4G19640.1 ; AT4G19640.1 ; AT4G19640 .
GeneIDi 827706.
KEGGi ath:AT4G19640.

Organism-specific databases

TAIRi AT4G19640.

Phylogenomic databases

eggNOGi COG1100.
HOGENOMi HOG000233968.
InParanoidi Q9SN68.
OMAi TNVKEIF.
PhylomeDBi Q9SN68.

Miscellaneous databases

EvolutionaryTracei Q9SN68.

Gene expression databases

ArrayExpressi Q9SN68.
Genevestigatori Q9SN68.

Family and domain databases

Gene3Di 3.40.50.300. 1 hit.
InterProi IPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view ]
Pfami PF00071. Ras. 1 hit.
[Graphical view ]
PRINTSi PR00449. RASTRNSFRMNG.
SMARTi SM00175. RAB. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 1 hit.
TIGRFAMsi TIGR00231. small_GTP. 1 hit.
PROSITEi PS51419. RAB. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Ara6, a plant-unique novel type Rab GTPase, functions in the endocytic pathway of Arabidopsis thaliana."
    Ueda T., Yamaguchi M., Uchimiya H., Nakano A.
    EMBO J. 20:4730-4741(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, TISSUE SPECIFICITY, MUTAGENESIS OF GLN-69.
  2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Analysis of the small GTPase gene superfamily of Arabidopsis."
    Vernoud V., Horton A.C., Yang Z., Nielsen E.
    Plant Physiol. 131:1191-1208(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.
  6. "The Arabidopsis rab5 homologs rha1 and ara7 localize to the prevacuolar compartment."
    Lee G.J., Sohn E.J., Lee M.H., Hwang I.
    Plant Cell Physiol. 45:1211-1220(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  7. "Two plant-viral movement proteins traffic in the endocytic recycling pathway."
    Haupt S., Cowan G.H., Ziegler A., Roberts A.G., Oparka K.J., Torrance L.
    Plant Cell 17:164-181(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  8. "Endocytosis and degradation of BOR1, a boron transporter of Arabidopsis thaliana, regulated by boron availability."
    Takano J., Miwa K., Yuan L., von Wiren N., Fujiwara T.
    Proc. Natl. Acad. Sci. U.S.A. 102:12276-12281(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  9. "VPS9a, the common activator for two distinct types of Rab5 GTPases, is essential for the development of Arabidopsis thaliana."
    Goh T., Uchida W., Arakawa S., Ito E., Dainobu T., Ebine K., Takeuchi M., Sato K., Ueda T., Nakano A.
    Plant Cell 19:3504-3515(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH VPS9A, INDUCTION.
  10. "PROTEIN S-ACYL TRANSFERASE10 Is Critical for Development and Salt Tolerance in Arabidopsis."
    Zhou L.Z., Li S., Feng Q.N., Zhang Y.L., Zhao X., Zeng Y.L., Wang H., Jiang L., Zhang Y.
    Plant Cell 25:1093-1107(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  11. "GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5.Vps9 system."
    Uejima T., Ihara K., Goh T., Ito E., Sunada M., Ueda T., Nakano A., Wakatsuki S.
    J. Biol. Chem. 285:36689-36697(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF 1-179 IN COMPLEX WITH GDP, FUNCTION, INTERACTION WITH VPS9A, MUTAGENESIS OF VAL-19; SER-24; VAL-36; THR-42; GLY-44; ALA-46; PHE-47; TRP-64; ALA-67; GLN-69; SER-74; LEU-75; MET-78; TYR-79 AND ASN-123.

Entry informationi

Entry nameiRAF2B_ARATH
AccessioniPrimary (citable) accession number: Q9SN68
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 5, 2011
Last sequence update: May 1, 2000
Last modified: June 11, 2014
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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