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Protein

Rabphilin-3A

Gene

Rph3a

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Protein transport. Probably involved with Ras-related protein Rab-3A in synaptic vesicle traffic and/or synaptic vesicle fusion. Could play a role in neurotransmitter release by regulating membrane flow in the nerve terminal.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi412 – 4121Calcium 1; via carbonyl oxygenBy similarity
Metal bindingi413 – 4131Calcium 1Combined sources
Metal bindingi413 – 4131Calcium 2By similarity
Metal bindingi419 – 4191Calcium 2By similarity
Metal bindingi474 – 4741Calcium 1By similarity
Metal bindingi474 – 4741Calcium 2By similarity
Metal bindingi475 – 4751Calcium 2; via carbonyl oxygenBy similarity
Metal bindingi476 – 4761Calcium 1Combined sources
Metal bindingi476 – 4761Calcium 2By similarity
Metal bindingi482 – 4821Calcium 1By similarity
Metal bindingi529 – 5291Calcium 3; via carbonyl oxygenCombined sources1 Publication
Metal bindingi571 – 5711Calcium 3Combined sources1 Publication
Metal bindingi571 – 5711Calcium 4Combined sources1 Publication
Metal bindingi577 – 5771Calcium 3Combined sources1 Publication
Metal bindingi631 – 6311Calcium 3Combined sources1 Publication
Metal bindingi631 – 6311Calcium 4Combined sources1 Publication
Metal bindingi632 – 6321Calcium 3; via carbonyl oxygenCombined sources1 Publication
Metal bindingi633 – 6331Calcium 3Combined sources1 Publication
Metal bindingi633 – 6331Calcium 4Combined sources1 Publication
Metal bindingi639 – 6391Calcium 4Combined sources1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri88 – 14558FYVE-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • calcium-dependent phospholipid binding Source: UniProtKB
  • calcium ion binding Source: UniProtKB
  • clathrin binding Source: GO_Central
  • inositol 1,4,5 trisphosphate binding Source: RGD
  • phosphate ion binding Source: RGD
  • phosphatidylinositol-4,5-bisphosphate binding Source: RGD
  • phospholipid binding Source: RGD
  • protein complex binding Source: RGD
  • selenium binding Source: RGD
  • syntaxin binding Source: GO_Central
  • zinc ion binding Source: RGD

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Keywords - Ligandi

Calcium, Lipid-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Rabphilin-3A
Alternative name(s):
Exophilin-1
Gene namesi
Name:Rph3a
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi620073. Rph3a.

Subcellular locationi

GO - Cellular componenti

  • cell junction Source: UniProtKB-KW
  • cytosol Source: RGD
  • extrinsic component of membrane Source: RGD
  • neuron projection Source: RGD
  • plasma membrane Source: GO_Central
  • protein complex Source: RGD
  • secretory granule Source: RGD
  • synapse Source: RGD
  • synaptic vesicle Source: RGD
  • synaptic vesicle membrane Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Membrane, Synapse

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 684684Rabphilin-3APRO_0000190229Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei274 – 2741PhosphoserineBy similarity
Modified residuei682 – 6821PhosphoserineCombined sources
Modified residuei683 – 6831PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP47709.
PRIDEiP47709.

PTM databases

iPTMnetiP47709.
PhosphoSiteiP47709.

Miscellaneous databases

PMAP-CutDBP47709.

Expressioni

Tissue specificityi

Specifically expressed in brain.

Interactioni

Subunit structurei

Interacts with RAB3B, RAB3C, RAB3D, RAB8A, RAB27A and RAB27B (By similarity). Interacts with RAB3A. Monomer.By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Rab3aP630122EBI-1027524,EBI-440126
Snap25P608814EBI-1027524,EBI-1027214

GO - Molecular functioni

  • clathrin binding Source: GO_Central
  • protein complex binding Source: RGD
  • syntaxin binding Source: GO_Central

Protein-protein interaction databases

IntActiP47709. 3 interactions.
MINTiMINT-85841.
STRINGi10116.ENSRNOP00000001844.

Structurei

Secondary structure

1
684
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi50 – 8435Combined sources
Beta strandi90 – 934Combined sources
Beta strandi95 – 973Combined sources
Beta strandi108 – 1103Combined sources
Turni112 – 1143Combined sources
Beta strandi117 – 1193Combined sources
Beta strandi122 – 1254Combined sources
Beta strandi129 – 1324Combined sources
Beta strandi135 – 1373Combined sources
Helixi138 – 14912Combined sources
Helixi152 – 1554Combined sources
Beta strandi385 – 3939Combined sources
Helixi394 – 3963Combined sources
Beta strandi398 – 40811Combined sources
Beta strandi414 – 4163Combined sources
Beta strandi420 – 4289Combined sources
Helixi432 – 4343Combined sources
Beta strandi435 – 4373Combined sources
Beta strandi448 – 45710Combined sources
Helixi460 – 4656Combined sources
Beta strandi467 – 4759Combined sources
Beta strandi477 – 4793Combined sources
Beta strandi481 – 49010Combined sources
Helixi491 – 4933Combined sources
Beta strandi500 – 5056Combined sources
Helixi527 – 5304Combined sources
Beta strandi543 – 5519Combined sources
Turni552 – 5554Combined sources
Beta strandi556 – 56611Combined sources
Beta strandi578 – 5858Combined sources
Beta strandi593 – 5953Combined sources
Beta strandi606 – 6149Combined sources
Helixi617 – 6226Combined sources
Beta strandi624 – 6318Combined sources
Beta strandi634 – 6363Combined sources
Beta strandi639 – 6479Combined sources
Helixi652 – 66312Combined sources
Beta strandi664 – 6674Combined sources
Beta strandi669 – 6746Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZBDX-ray2.60B41-170[»]
2CHDX-ray1.92A371-510[»]
2CM5X-ray1.28A519-684[»]
2CM6X-ray1.85A/B519-684[»]
3RPBNMR-A541-680[»]
4LT7X-ray2.50A378-510[»]
4NP9X-ray1.92A378-510[»]
4NS0X-ray1.80A378-510[»]
ProteinModelPortaliP47709.
SMRiP47709. Positions 44-167, 382-509, 541-680.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP47709.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini40 – 157118RabBDPROSITE-ProRule annotationAdd
BLAST
Domaini384 – 488105C2 1PROSITE-ProRule annotationAdd
BLAST
Domaini542 – 645104C2 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi280 – 36485Pro-richAdd
BLAST

Domaini

Binds calcium via the C2 domains. The calcium-bound C2 domains mediate interactions with phospholipid bilayers.1 Publication

Sequence similaritiesi

Contains 2 C2 domains.PROSITE-ProRule annotation
Contains 1 FYVE-type zinc finger.PROSITE-ProRule annotation
Contains 1 RabBD (Rab-binding) domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri88 – 14558FYVE-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1013. Eukaryota.
ENOG410XQXA. LUCA.
HOGENOMiHOG000294226.
HOVERGENiHBG017739.
InParanoidiP47709.
KOiK19938.
PhylomeDBiP47709.

Family and domain databases

Gene3Di2.60.40.150. 2 hits.
3.30.40.10. 1 hit.
InterProiIPR000008. C2_dom.
IPR010911. Rab_BD.
IPR028698. RPH3A.
IPR001565. Synaptotagmin.
IPR017455. Znf_FYVE-rel.
IPR011011. Znf_FYVE_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PANTHERiPTHR10024:SF118. PTHR10024:SF118. 1 hit.
PfamiPF00168. C2. 2 hits.
PF02318. FYVE_2. 1 hit.
[Graphical view]
PRINTSiPR00360. C2DOMAIN.
PR00399. SYNAPTOTAGMN.
SMARTiSM00239. C2. 2 hits.
[Graphical view]
SUPFAMiSSF49562. SSF49562. 2 hits.
SSF57903. SSF57903. 1 hit.
PROSITEiPS50004. C2. 2 hits.
PS50916. RABBD. 1 hit.
PS50178. ZF_FYVE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P47709-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTDTVVNRWM YPGDGPLQSN DKEQLQAGWS VHPGAQTDRQ RKQEELTDEE
60 70 80 90 100
KEIINRVIAR AEKMETMEQE RIGRLVDRLE TMRKNVAGDG VNRCILCGEQ
110 120 130 140 150
LGMLGSACVV CEDCKKNVCT KCGVETSNNR PHPVWLCKIC LEQREVWKRS
160 170 180 190 200
GAWFFKGFPK QVLPQPMPIK KTKPQQPAGE PATQEQPTPE SRHPARAPAR
210 220 230 240 250
GDMEDRRAPG QKPGPDLTSA PGRGSHGPPT RRASEARMST TTRDSEGWDH
260 270 280 290 300
GHGGGAGDTS RSPGGEQGLR RANSVQASRP APASMPSPAP PQPVQPGPPG
310 320 330 340 350
GSRAAPGPGR FPEQSTEAPP SDPGYPGAVA PAREERTGPT GGFQAAPHTA
360 370 380 390 400
GPYSQAAPAR QPPPAEEEEE EANSYDSDQA TTLGALEFSL LYDQDNSNLQ
410 420 430 440 450
CTIIRAKGLK PMDSNGLADP YVKLHLLPGA SKSNKLRTKT LRNTRNPVWN
460 470 480 490 500
ETLQYHGITE EDMQRKTLRI SVCDEDKFGH NEFIGETRFS LKKLKANQRK
510 520 530 540 550
NFNICLERVI PMKRAGTTGS ARGMALYEEE QVERIGDIEE RGKILVSLMY
560 570 580 590 600
STQQGGLIVG IIRCVHLAAM DANGYSDPFV KLWLKPDMGK KAKHKTQIKK
610 620 630 640 650
KTLNPEFNEE FFYDIKHSDL AKKSLDISVW DYDIGKSNDY IGGCQLGISA
660 670 680
KGERLKHWYE CLKNKDKKIE RWHQLQNENH VSSD
Length:684
Mass (Da):75,832
Last modified:February 1, 1996 - v1
Checksum:i05838BC3C7A86444
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U12571 mRNA. Translation: AAA62662.1.
PIRiI58166.
RefSeqiNP_598202.1. NM_133518.1.
UniGeneiRn.10976.

Genome annotation databases

GeneIDi171039.
KEGGirno:171039.
UCSCiRGD:620073. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U12571 mRNA. Translation: AAA62662.1.
PIRiI58166.
RefSeqiNP_598202.1. NM_133518.1.
UniGeneiRn.10976.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZBDX-ray2.60B41-170[»]
2CHDX-ray1.92A371-510[»]
2CM5X-ray1.28A519-684[»]
2CM6X-ray1.85A/B519-684[»]
3RPBNMR-A541-680[»]
4LT7X-ray2.50A378-510[»]
4NP9X-ray1.92A378-510[»]
4NS0X-ray1.80A378-510[»]
ProteinModelPortaliP47709.
SMRiP47709. Positions 44-167, 382-509, 541-680.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP47709. 3 interactions.
MINTiMINT-85841.
STRINGi10116.ENSRNOP00000001844.

PTM databases

iPTMnetiP47709.
PhosphoSiteiP47709.

Proteomic databases

PaxDbiP47709.
PRIDEiP47709.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi171039.
KEGGirno:171039.
UCSCiRGD:620073. rat.

Organism-specific databases

CTDi22895.
RGDi620073. Rph3a.

Phylogenomic databases

eggNOGiKOG1013. Eukaryota.
ENOG410XQXA. LUCA.
HOGENOMiHOG000294226.
HOVERGENiHBG017739.
InParanoidiP47709.
KOiK19938.
PhylomeDBiP47709.

Miscellaneous databases

EvolutionaryTraceiP47709.
PMAP-CutDBP47709.
PROiP47709.

Family and domain databases

Gene3Di2.60.40.150. 2 hits.
3.30.40.10. 1 hit.
InterProiIPR000008. C2_dom.
IPR010911. Rab_BD.
IPR028698. RPH3A.
IPR001565. Synaptotagmin.
IPR017455. Znf_FYVE-rel.
IPR011011. Znf_FYVE_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PANTHERiPTHR10024:SF118. PTHR10024:SF118. 1 hit.
PfamiPF00168. C2. 2 hits.
PF02318. FYVE_2. 1 hit.
[Graphical view]
PRINTSiPR00360. C2DOMAIN.
PR00399. SYNAPTOTAGMN.
SMARTiSM00239. C2. 2 hits.
[Graphical view]
SUPFAMiSSF49562. SSF49562. 2 hits.
SSF57903. SSF57903. 1 hit.
PROSITEiPS50004. C2. 2 hits.
PS50916. RABBD. 1 hit.
PS50178. ZF_FYVE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Synaptic targeting of rabphilin-3A, a synaptic vesicle Ca2+/phospholipid-binding protein, depends on rab3A/3C."
    Li C., Takei K., Geppert M., Daniell L., Stenius K., Chapman E.R., Jahn R., de Camilli P., Suedhof T.C.
    Neuron 13:885-898(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues."
    Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C., Olsen J.V.
    Nat. Commun. 3:876-876(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-682 AND SER-683, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  3. "Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A."
    Ostermeier C., Brunger A.T.
    Cell 96:363-374(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 41-170 IN COMPLEX WITH RAB3A.
    Tissue: Brain.
  4. "Structure of the Janus-faced C2B domain of rabphilin."
    Ubach J., Garcia J., Nittler M.P., Sudhof T.C., Rizo J.
    Nat. Cell Biol. 1:106-112(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 541-680.
  5. "The C2A-C2B linker defines the high affinity Ca(2+) binding mode of rabphilin-3A."
    Montaville P., Schlicker C., Leonov A., Zweckstetter M., Sheldrick G.M., Becker S.
    J. Biol. Chem. 282:5015-5025(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.28 ANGSTROMS) OF 519-684 IN COMPLEX WITH CALCIUM IONS, DOMAIN, SUBCELLULAR LOCATION, CALCIUM-BINDING.

Entry informationi

Entry nameiRP3A_RAT
AccessioniPrimary (citable) accession number: P47709
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: July 6, 2016
This is version 139 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.