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Protein

RUN and FYVE domain-containing protein 1

Gene

RUFY1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Binds phospholipid vesicles containing phosphatidylinositol 3-phosphate and participates in early endosomal trafficking.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri642 – 700FYVE-typePROSITE-ProRule annotationAdd BLAST59

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Endocytosis, Protein transport, Transport

Keywords - Ligandi

Lipid-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000176783-MONOMER.
ReactomeiR-HSA-1660499. Synthesis of PIPs at the plasma membrane.

Names & Taxonomyi

Protein namesi
Recommended name:
RUN and FYVE domain-containing protein 1
Alternative name(s):
FYVE-finger protein EIP1
La-binding protein 1
Rab4-interacting protein
Zinc finger FYVE domain-containing protein 12
Gene namesi
Name:RUFY1
Synonyms:RABIP4, ZFYVE12
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:19760. RUFY1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi389Y → F: Abolishes phosphorylation and endosomal targeting; when associated with F-400. 1 Publication1
Mutagenesisi400Y → F: Abolishes phosphorylation and endosomal targeting; when associated with F-389. 1 Publication1

Organism-specific databases

DisGeNETi80230.
OpenTargetsiENSG00000176783.
PharmGKBiPA134944787.

Polymorphism and mutation databases

BioMutaiRUFY1.
DMDMi110282993.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000975301 – 708RUN and FYVE domain-containing protein 1Add BLAST708

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei389Phosphotyrosine1 Publication1
Modified residuei400Phosphotyrosine1 Publication1
Modified residuei620PhosphoserineCombined sources1

Post-translational modificationi

Phosphorylation on Tyr-389 and/or Tyr-400 is required for interaction with BMX and endosomal targeting.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ96T51.
MaxQBiQ96T51.
PaxDbiQ96T51.
PeptideAtlasiQ96T51.
PRIDEiQ96T51.

PTM databases

iPTMnetiQ96T51.
PhosphoSitePlusiQ96T51.

Expressioni

Tissue specificityi

Broadly expressed, with highest levels in lung, testis, kidney and brain.1 Publication

Gene expression databases

BgeeiENSG00000176783.
CleanExiHS_RUFY1.
ExpressionAtlasiQ96T51. baseline and differential.
GenevisibleiQ96T51. HS.

Organism-specific databases

HPAiHPA038804.
HPA057614.

Interactioni

Subunit structurei

Interacts with BMX. May interact with SSB. Interacts with RAB4 and RAB5 that have been activated by GTP-binding.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
DIEXFQ68CQ43EBI-3941207,EBI-747711
PIAS2O759283EBI-3941207,EBI-348555
RAB39BQ96DA23EBI-3941207,EBI-9089467
RAB3IPQ96QF03EBI-3941207,EBI-747844
TXNDC17Q9BRA23EBI-3941207,EBI-1055906

Protein-protein interaction databases

BioGridi123193. 57 interactors.
IntActiQ96T51. 14 interactors.
MINTiMINT-7302811.
STRINGi9606.ENSP00000325594.

Structurei

Secondary structure

1708
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni649 – 651Combined sources3
Beta strandi657 – 659Combined sources3
Beta strandi661 – 663Combined sources3
Turni665 – 667Combined sources3
Beta strandi670 – 672Combined sources3
Helixi674 – 676Combined sources3
Beta strandi678 – 680Combined sources3
Beta strandi683 – 687Combined sources5
Beta strandi689 – 691Combined sources3
Helixi693 – 698Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YQMNMR-A627-708[»]
2YW8X-ray3.00A627-708[»]
ProteinModelPortaliQ96T51.
SMRiQ96T51.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96T51.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini139 – 271RUNPROSITE-ProRule annotationAdd BLAST133

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni615 – 625Interaction with RAB4By similarityAdd BLAST11

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili321 – 374Sequence analysisAdd BLAST54
Coiled coili405 – 617Sequence analysisAdd BLAST213

Domaini

The FYVE-type zinc finger domain mediates interactions with phosphatidylinositol 3-phosphate in membranes of early endosomes and penetrates bilayers. The FYVE domain insertion into PtdIns3P-enriched membranes is substantially increased in acidic conditions.1 Publication

Sequence similaritiesi

Contains 1 FYVE-type zinc finger.PROSITE-ProRule annotation
Contains 1 RUN domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri642 – 700FYVE-typePROSITE-ProRule annotationAdd BLAST59

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

eggNOGiKOG1729. Eukaryota.
KOG4381. Eukaryota.
ENOG410XRAX. LUCA.
GeneTreeiENSGT00550000074558.
HOVERGENiHBG057053.
InParanoidiQ96T51.
KOiK12482.
OMAiAILDQKH.
OrthoDBiEOG091G042J.
PhylomeDBiQ96T51.
TreeFamiTF323904.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR004012. Run_dom.
IPR000306. Znf_FYVE.
IPR017455. Znf_FYVE-rel.
IPR011011. Znf_FYVE_PHD.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF01363. FYVE. 1 hit.
PF02759. RUN. 1 hit.
[Graphical view]
SMARTiSM00064. FYVE. 1 hit.
SM00593. RUN. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS50826. RUN. 1 hit.
PS50178. ZF_FYVE. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q96T51-1) [UniParc]FASTAAdd to basket
Also known as: rabip4'

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
MADREGGCAA GRGRELEPEL EPGPGPGSAL EPGEEFEIVD RSQLPGPGDL
60 70 80 90 100
RSATRPRAAE GWSAPILTLA RRATGNLSAS CGSALRAAAG LGGGDSGDGT
110 120 130 140 150
ARAASKCQMM EERANLMHMM KLSIKVLLQS ALSLGRSLDA DHAPLQQFFV
160 170 180 190 200
VMEHCLKHGL KVKKSFIGQN KSFFGPLELV EKLCPEASDI ATSVRNLPEL
210 220 230 240 250
KTAVGRGRAW LYLALMQKKL ADYLKVLIDN KHLLSEFYEP EALMMEEEGM
260 270 280 290 300
VIVGLLVGLN VLDANLCLKG EDLDSQVGVI DFSLYLKDVQ DLDGGKEHER
310 320 330 340 350
ITDVLDQKNY VEELNRHLSC TVGDLQTKID GLEKTNSKLQ EELSAATDRI
360 370 380 390 400
CSLQEEQQQL REQNELIRER SEKSVEITKQ DTKVELETYK QTRQGLDEMY
410 420 430 440 450
SDVWKQLKEE KKVRLELEKE LELQIGMKTE MEIAMKLLEK DTHEKQDTLV
460 470 480 490 500
ALRQQLEEVK AINLQMFHKA QNAESSLQQK NEAITSFEGK TNQVMSSMKQ
510 520 530 540 550
MEERLQHSER ARQGAEERSH KLQQELGGRI GALQLQLSQL HEQCSSLEKE
560 570 580 590 600
LKSEKEQRQA LQRELQHEKD TSSLLRMELQ QVEGLKKELR ELQDEKAELQ
610 620 630 640 650
KICEEQEQAL QEMGLHLSQS KLKMEDIKEV NQALKGHAWL KDDEATHCRQ
660 670 680 690 700
CEKEFSISRR KHHCRNCGHI FCNTCSSNEL ALPSYPKPVR VCDSCHTLLL

QRCSSTAS
Length:708
Mass (Da):79,818
Last modified:July 11, 2006 - v2
Checksum:i6697B4BC108AD54F
GO
Isoform 2 (identifier: Q96T51-2) [UniParc]FASTAAdd to basket
Also known as: rabip4

The sequence of this isoform differs from the canonical sequence as follows:
     1-108: Missing.

Show »
Length:600
Mass (Da):69,078
Checksum:i44EEEB383C18FC47
GO
Isoform 3 (identifier: Q96T51-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     343-412: LSAATDRICS...VWKQLKEEKK → EERMKGQDKG...RRTAAVKRTK
     413-708: Missing.

Note: No experimental confirmation available.
Show »
Length:412
Mass (Da):44,489
Checksum:iDB0F4DA2BD8EEA83
GO

Sequence cautioni

The sequence AAK50771 differs from that shown. Reason: Frameshift at positions 47 and 88.Curated
The sequence BAB15276 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti519 – 528SHKLQQELGG → TTSCSRSWAV in AAQ14554 (PubMed:14617813).Curated10
Sequence conflicti570D → N in AAQ14554 (PubMed:14617813).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_035985267C → F in a breast cancer sample; somatic mutation. 1 Publication1
Natural variantiVAR_051327298H → Q.Corresponds to variant rs6879322dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0197851 – 108Missing in isoform 2. 2 PublicationsAdd BLAST108
Alternative sequenceiVSP_019786343 – 412LSAAT…KEEKK → EERMKGQDKGGLSRGRELAA SCPAVSLLDTSCLLLAGGGC SALLRLSTAFSCNRPNLLTS RRTAAVKRTK in isoform 3. 1 PublicationAdd BLAST70
Alternative sequenceiVSP_019787413 – 708Missing in isoform 3. 1 PublicationAdd BLAST296

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF312367 mRNA. Translation: AAQ14554.1.
AK025904 mRNA. Translation: BAB15276.1. Different initiation.
AK075021 mRNA. No translation available.
BC032571 mRNA. Translation: AAH32571.1.
AF361055 mRNA. Translation: AAK50771.1. Frameshift.
AB209507 mRNA. Translation: BAD92744.1.
CCDSiCCDS34312.1. [Q96T51-2]
CCDS4445.2. [Q96T51-1]
RefSeqiNP_001035541.1. NM_001040451.2. [Q96T51-2]
NP_001035542.1. NM_001040452.2. [Q96T51-2]
NP_079434.3. NM_025158.4. [Q96T51-1]
XP_016865384.1. XM_017009895.1.
UniGeneiHs.306769.

Genome annotation databases

EnsembliENST00000319449; ENSP00000325594; ENSG00000176783. [Q96T51-1]
ENST00000393438; ENSP00000377087; ENSG00000176783. [Q96T51-2]
ENST00000437570; ENSP00000390025; ENSG00000176783. [Q96T51-2]
GeneIDi80230.
KEGGihsa:80230.
UCSCiuc003mka.3. human. [Q96T51-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF312367 mRNA. Translation: AAQ14554.1.
AK025904 mRNA. Translation: BAB15276.1. Different initiation.
AK075021 mRNA. No translation available.
BC032571 mRNA. Translation: AAH32571.1.
AF361055 mRNA. Translation: AAK50771.1. Frameshift.
AB209507 mRNA. Translation: BAD92744.1.
CCDSiCCDS34312.1. [Q96T51-2]
CCDS4445.2. [Q96T51-1]
RefSeqiNP_001035541.1. NM_001040451.2. [Q96T51-2]
NP_001035542.1. NM_001040452.2. [Q96T51-2]
NP_079434.3. NM_025158.4. [Q96T51-1]
XP_016865384.1. XM_017009895.1.
UniGeneiHs.306769.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YQMNMR-A627-708[»]
2YW8X-ray3.00A627-708[»]
ProteinModelPortaliQ96T51.
SMRiQ96T51.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123193. 57 interactors.
IntActiQ96T51. 14 interactors.
MINTiMINT-7302811.
STRINGi9606.ENSP00000325594.

PTM databases

iPTMnetiQ96T51.
PhosphoSitePlusiQ96T51.

Polymorphism and mutation databases

BioMutaiRUFY1.
DMDMi110282993.

Proteomic databases

EPDiQ96T51.
MaxQBiQ96T51.
PaxDbiQ96T51.
PeptideAtlasiQ96T51.
PRIDEiQ96T51.

Protocols and materials databases

DNASUi80230.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000319449; ENSP00000325594; ENSG00000176783. [Q96T51-1]
ENST00000393438; ENSP00000377087; ENSG00000176783. [Q96T51-2]
ENST00000437570; ENSP00000390025; ENSG00000176783. [Q96T51-2]
GeneIDi80230.
KEGGihsa:80230.
UCSCiuc003mka.3. human. [Q96T51-1]

Organism-specific databases

CTDi80230.
DisGeNETi80230.
GeneCardsiRUFY1.
HGNCiHGNC:19760. RUFY1.
HPAiHPA038804.
HPA057614.
MIMi610327. gene.
neXtProtiNX_Q96T51.
OpenTargetsiENSG00000176783.
PharmGKBiPA134944787.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1729. Eukaryota.
KOG4381. Eukaryota.
ENOG410XRAX. LUCA.
GeneTreeiENSGT00550000074558.
HOVERGENiHBG057053.
InParanoidiQ96T51.
KOiK12482.
OMAiAILDQKH.
OrthoDBiEOG091G042J.
PhylomeDBiQ96T51.
TreeFamiTF323904.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000176783-MONOMER.
ReactomeiR-HSA-1660499. Synthesis of PIPs at the plasma membrane.

Miscellaneous databases

ChiTaRSiRUFY1. human.
EvolutionaryTraceiQ96T51.
GeneWikiiRUFY1.
GenomeRNAii80230.
PROiQ96T51.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000176783.
CleanExiHS_RUFY1.
ExpressionAtlasiQ96T51. baseline and differential.
GenevisibleiQ96T51. HS.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR004012. Run_dom.
IPR000306. Znf_FYVE.
IPR017455. Znf_FYVE-rel.
IPR011011. Znf_FYVE_PHD.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF01363. FYVE. 1 hit.
PF02759. RUN. 1 hit.
[Graphical view]
SMARTiSM00064. FYVE. 1 hit.
SM00593. RUN. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS50826. RUN. 1 hit.
PS50178. ZF_FYVE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRUFY1_HUMAN
AccessioniPrimary (citable) accession number: Q96T51
Secondary accession number(s): Q59FF3, Q71S93, Q9H6I3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 13, 2004
Last sequence update: July 11, 2006
Last modified: November 30, 2016
This is version 142 of the entry and version 2 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 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.