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Q96T51

- RUFY1_HUMAN

UniProt

Q96T51 - RUFY1_HUMAN

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Protein

RUN and FYVE domain-containing protein 1

Gene
RUFY1, RABIP4, ZFYVE12
Organism
Homo sapiens (Human)
Status
Reviewed - 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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri642 – 70059FYVE-typeAdd
BLAST

GO - Molecular functioni

  1. lipid binding Source: UniProtKB-KW
  2. protein binding Source: IntAct
  3. protein transporter activity Source: Ensembl
  4. zinc ion binding Source: InterPro

GO - Biological processi

  1. endocytosis Source: UniProtKB-KW
  2. regulation of endocytosis Source: Ensembl
Complete GO annotation...

Keywords - Biological processi

Endocytosis, Protein transport, Transport

Keywords - Ligandi

Lipid-binding, Metal-binding, Zinc

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
ProteomesiUP000005640: Chromosome 5

Organism-specific databases

HGNCiHGNC:19760. RUFY1.

Subcellular locationi

Cytoplasm. Early endosome membrane; Peripheral membrane protein 2 Publications

GO - Cellular componenti

  1. cytoplasm Source: HPA
  2. early endosome membrane Source: UniProtKB-SubCell
  3. intracellular membrane-bounded organelle Source: HPA
  4. nucleus Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi389 – 3891Y → F: Abolishes phosphorylation and endosomal targeting; when associated with F-400. 1 Publication
Mutagenesisi400 – 4001Y → F: Abolishes phosphorylation and endosomal targeting; when associated with F-389. 1 Publication

Organism-specific databases

PharmGKBiPA134944787.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 708708RUN and FYVE domain-containing protein 1PRO_0000097530Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei389 – 3891Phosphotyrosine1 Publication
Modified residuei400 – 4001Phosphotyrosine1 Publication

Post-translational modificationi

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

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ96T51.
PaxDbiQ96T51.
PRIDEiQ96T51.

PTM databases

PhosphoSiteiQ96T51.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiQ96T51.
CleanExiHS_RUFY1.
GenevestigatoriQ96T51.

Organism-specific databases

HPAiHPA038804.

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
PIAS2O759283EBI-3941207,EBI-348555

Protein-protein interaction databases

BioGridi123193. 23 interactions.
IntActiQ96T51. 4 interactions.
MINTiMINT-7302811.
STRINGi9606.ENSP00000377094.

Structurei

Secondary structure

1
708
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni649 – 6513
Beta strandi657 – 6593
Beta strandi661 – 6633
Turni665 – 6673
Beta strandi670 – 6723
Helixi674 – 6763
Beta strandi678 – 6803
Beta strandi683 – 6875
Beta strandi689 – 6913
Helixi693 – 6986

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2YQMNMR-A627-708[»]
2YW8X-ray3.00A627-708[»]
ProteinModelPortaliQ96T51.
SMRiQ96T51. Positions 109-275, 588-708.

Miscellaneous databases

EvolutionaryTraceiQ96T51.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini139 – 271133RUNAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni615 – 62511Interaction with RAB4 By similarityAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili321 – 37454 Reviewed predictionAdd
BLAST
Coiled coili405 – 617213 Reviewed predictionAdd
BLAST

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 RUN domain.

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

eggNOGiNOG270133.
HOVERGENiHBG057053.
InParanoidiQ96T51.
KOiK12482.
OMAiMMKLSVK.
OrthoDBiEOG722J98.
PhylomeDBiQ96T51.
TreeFamiTF323904.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR004012. Run.
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. Align

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

MADREGGCAA GRGRELEPEL EPGPGPGSAL EPGEEFEIVD RSQLPGPGDL    50
RSATRPRAAE GWSAPILTLA RRATGNLSAS CGSALRAAAG LGGGDSGDGT 100
ARAASKCQMM EERANLMHMM KLSIKVLLQS ALSLGRSLDA DHAPLQQFFV 150
VMEHCLKHGL KVKKSFIGQN KSFFGPLELV EKLCPEASDI ATSVRNLPEL 200
KTAVGRGRAW LYLALMQKKL ADYLKVLIDN KHLLSEFYEP EALMMEEEGM 250
VIVGLLVGLN VLDANLCLKG EDLDSQVGVI DFSLYLKDVQ DLDGGKEHER 300
ITDVLDQKNY VEELNRHLSC TVGDLQTKID GLEKTNSKLQ EELSAATDRI 350
CSLQEEQQQL REQNELIRER SEKSVEITKQ DTKVELETYK QTRQGLDEMY 400
SDVWKQLKEE KKVRLELEKE LELQIGMKTE MEIAMKLLEK DTHEKQDTLV 450
ALRQQLEEVK AINLQMFHKA QNAESSLQQK NEAITSFEGK TNQVMSSMKQ 500
MEERLQHSER ARQGAEERSH KLQQELGGRI GALQLQLSQL HEQCSSLEKE 550
LKSEKEQRQA LQRELQHEKD TSSLLRMELQ QVEGLKKELR ELQDEKAELQ 600
KICEEQEQAL QEMGLHLSQS KLKMEDIKEV NQALKGHAWL KDDEATHCRQ 650
CEKEFSISRR KHHCRNCGHI FCNTCSSNEL ALPSYPKPVR VCDSCHTLLL 700
QRCSSTAS 708
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 AAK50771.1 differs from that shown. Reason: Frameshift at positions 47 and 88.
The sequence BAB15276.1 differs from that shown. Reason: Erroneous initiation.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti267 – 2671C → F in a breast cancer sample; somatic mutation. 1 Publication
VAR_035985
Natural varianti298 – 2981H → Q.
Corresponds to variant rs6879322 [ dbSNP | Ensembl ].
VAR_051327

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 108108Missing in isoform 2. VSP_019785Add
BLAST
Alternative sequencei343 – 41270LSAAT…KEEKK → EERMKGQDKGGLSRGRELAA SCPAVSLLDTSCLLLAGGGC SALLRLSTAFSCNRPNLLTS RRTAAVKRTK in isoform 3. VSP_019786Add
BLAST
Alternative sequencei413 – 708296Missing in isoform 3. VSP_019787Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti519 – 52810SHKLQQELGG → TTSCSRSWAV in AAQ14554. 1 Publication
Sequence conflicti570 – 5701D → N in AAQ14554. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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]
UniGeneiHs.306769.

Genome annotation databases

EnsembliENST00000319449; ENSP00000325594; ENSG00000176783. [Q96T51-1]
ENST00000377001; ENSP00000366200; ENSG00000176783. [Q96T51-3]
ENST00000393438; ENSP00000377087; ENSG00000176783. [Q96T51-2]
ENST00000437570; ENSP00000390025; ENSG00000176783. [Q96T51-2]
GeneIDi80230.
KEGGihsa:80230.
UCSCiuc003mka.2. human. [Q96T51-1]

Polymorphism databases

DMDMi110282993.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS34312.1. [Q96T51-2 ]
CCDS4445.2. [Q96T51-1 ]
RefSeqi NP_001035541.1. NM_001040451.2. [Q96T51-2 ]
NP_001035542.1. NM_001040452.2. [Q96T51-2 ]
NP_079434.3. NM_025158.4. [Q96T51-1 ]
UniGenei Hs.306769.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2YQM NMR - A 627-708 [» ]
2YW8 X-ray 3.00 A 627-708 [» ]
ProteinModelPortali Q96T51.
SMRi Q96T51. Positions 109-275, 588-708.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 123193. 23 interactions.
IntActi Q96T51. 4 interactions.
MINTi MINT-7302811.
STRINGi 9606.ENSP00000377094.

PTM databases

PhosphoSitei Q96T51.

Polymorphism databases

DMDMi 110282993.

Proteomic databases

MaxQBi Q96T51.
PaxDbi Q96T51.
PRIDEi Q96T51.

Protocols and materials databases

DNASUi 80230.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000319449 ; ENSP00000325594 ; ENSG00000176783 . [Q96T51-1 ]
ENST00000377001 ; ENSP00000366200 ; ENSG00000176783 . [Q96T51-3 ]
ENST00000393438 ; ENSP00000377087 ; ENSG00000176783 . [Q96T51-2 ]
ENST00000437570 ; ENSP00000390025 ; ENSG00000176783 . [Q96T51-2 ]
GeneIDi 80230.
KEGGi hsa:80230.
UCSCi uc003mka.2. human. [Q96T51-1 ]

Organism-specific databases

CTDi 80230.
GeneCardsi GC05P178977.
HGNCi HGNC:19760. RUFY1.
HPAi HPA038804.
MIMi 610327. gene.
neXtProti NX_Q96T51.
PharmGKBi PA134944787.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG270133.
HOVERGENi HBG057053.
InParanoidi Q96T51.
KOi K12482.
OMAi MMKLSVK.
OrthoDBi EOG722J98.
PhylomeDBi Q96T51.
TreeFami TF323904.

Miscellaneous databases

ChiTaRSi RUFY1. human.
EvolutionaryTracei Q96T51.
GeneWikii RUFY1.
GenomeRNAii 80230.
NextBioi 70661.
PROi Q96T51.
SOURCEi Search...

Gene expression databases

Bgeei Q96T51.
CleanExi HS_RUFY1.
Genevestigatori Q96T51.

Family and domain databases

Gene3Di 3.30.40.10. 1 hit.
InterProi IPR004012. Run.
IPR000306. Znf_FYVE.
IPR017455. Znf_FYVE-rel.
IPR011011. Znf_FYVE_PHD.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view ]
Pfami PF01363. FYVE. 1 hit.
PF02759. RUN. 1 hit.
[Graphical view ]
SMARTi SM00064. FYVE. 1 hit.
SM00593. RUN. 1 hit.
[Graphical view ]
SUPFAMi SSF57903. SSF57903. 1 hit.
PROSITEi PS50826. RUN. 1 hit.
PS50178. ZF_FYVE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH SSB; RAB4 AND RAB5, IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, FUNCTION.
  2. "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] (ISOFORM 2).
  3. "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 2).
    Tissue: Brain.
  4. "Interaction between tyrosine kinase Etk and a RUN-domain and FYVE-domain containing protein RUFY1. A possible role of Etk in regulation of vesicle trafficking."
    Yang J., Kim O., Wu J., Qiu Y.
    J. Biol. Chem. 277:30219-30226(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 7-708 (ISOFORM 1), TISSUE SPECIFICITY, SUBCELLULAR LOCATION, INTERACTION WITH BMX, PHOSPHORYLATION AT TYR-389 AND TYR-400, MUTAGENESIS OF TYR-389 AND TYR-400.
  5. Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S., Ohara O., Nagase T., Kikuno R.F.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 90-708 (ISOFORM 3).
    Tissue: Brain.
  6. Cited for: DOMAIN FYVE-TYPE ZINC-FINGER.
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Solution structure of the FYVE domain in zinc finger FYVE domain-containing protein 12."
    RIKEN structural genomics initiative (RSGI)
    Submitted (OCT-2007) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 627-708.
  9. Cited for: VARIANT [LARGE SCALE ANALYSIS] PHE-267.

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: July 9, 2014
This is version 118 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

External Data

Dasty 3

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