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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)DescriptionActionsGraphical viewLength
Metal bindingi412Calcium 1; via carbonyl oxygenBy similarity1
Metal bindingi413Calcium 1Combined sources1
Metal bindingi413Calcium 2By similarity1
Metal bindingi419Calcium 2By similarity1
Metal bindingi474Calcium 1By similarity1
Metal bindingi474Calcium 2By similarity1
Metal bindingi475Calcium 2; via carbonyl oxygenBy similarity1
Metal bindingi476Calcium 1Combined sources1
Metal bindingi476Calcium 2By similarity1
Metal bindingi482Calcium 1By similarity1
Metal bindingi529Calcium 3; via carbonyl oxygenCombined sources1 Publication1
Metal bindingi571Calcium 3Combined sources1 Publication1
Metal bindingi571Calcium 4Combined sources1 Publication1
Metal bindingi577Calcium 3Combined sources1 Publication1
Metal bindingi631Calcium 3Combined sources1 Publication1
Metal bindingi631Calcium 4Combined sources1 Publication1
Metal bindingi632Calcium 3; via carbonyl oxygenCombined sources1 Publication1
Metal bindingi633Calcium 3Combined sources1 Publication1
Metal bindingi633Calcium 4Combined sources1 Publication1
Metal bindingi639Calcium 4Combined sources1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri88 – 145FYVE-typePROSITE-ProRule annotationAdd BLAST58

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001902291 – 684Rabphilin-3AAdd BLAST684

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei223Omega-N-methylarginineBy similarity1
Modified residuei274PhosphoserineBy similarity1
Modified residuei682PhosphoserineCombined sources1
Modified residuei683PhosphoserineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

PaxDbiP47709.
PRIDEiP47709.

PTM databases

iPTMnetiP47709.
PhosphoSitePlusiP47709.

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 interactors.
MINTiMINT-85841.
STRINGi10116.ENSRNOP00000001844.

Structurei

Secondary structure

1684
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi50 – 84Combined sources35
Beta strandi90 – 93Combined sources4
Beta strandi95 – 97Combined sources3
Beta strandi108 – 110Combined sources3
Turni112 – 114Combined sources3
Beta strandi117 – 119Combined sources3
Beta strandi122 – 125Combined sources4
Beta strandi129 – 132Combined sources4
Beta strandi135 – 137Combined sources3
Helixi138 – 149Combined sources12
Helixi152 – 155Combined sources4
Beta strandi385 – 393Combined sources9
Helixi394 – 396Combined sources3
Beta strandi398 – 408Combined sources11
Beta strandi414 – 416Combined sources3
Beta strandi420 – 428Combined sources9
Helixi432 – 434Combined sources3
Beta strandi435 – 437Combined sources3
Beta strandi448 – 457Combined sources10
Helixi460 – 465Combined sources6
Beta strandi467 – 475Combined sources9
Beta strandi477 – 479Combined sources3
Beta strandi481 – 490Combined sources10
Helixi491 – 493Combined sources3
Beta strandi500 – 505Combined sources6
Helixi527 – 530Combined sources4
Beta strandi543 – 551Combined sources9
Turni552 – 555Combined sources4
Beta strandi556 – 566Combined sources11
Beta strandi578 – 585Combined sources8
Beta strandi593 – 595Combined sources3
Beta strandi606 – 614Combined sources9
Helixi617 – 622Combined sources6
Beta strandi624 – 631Combined sources8
Beta strandi634 – 636Combined sources3
Beta strandi639 – 647Combined sources9
Helixi652 – 663Combined sources12
Beta strandi664 – 667Combined sources4
Beta strandi669 – 674Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP47709.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini40 – 157RabBDPROSITE-ProRule annotationAdd BLAST118
Domaini384 – 488C2 1PROSITE-ProRule annotationAdd BLAST105
Domaini542 – 645C2 2PROSITE-ProRule annotationAdd BLAST104

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi280 – 364Pro-richAdd BLAST85

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)DescriptionActionsGraphical viewLength
Zinc fingeri88 – 145FYVE-typePROSITE-ProRule annotationAdd BLAST58

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiP47709.
PhosphoSitePlusiP47709.

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...

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: November 2, 2016
This is version 141 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.