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Protein

E3 ubiquitin-protein ligase TRIM4

Gene

TRIM4

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

Functioni

E3 ubiquitin-protein ligase. Mediates 'Lys-63'-linked polyubiquitination of the innate immune receptor DDX58, this linkage doesn't lead to proteasomal degradation but seems to enhance IFN induction.1 Publication

Pathway:iprotein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri12 – 5342RING-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri82 – 12342B box-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • innate immune response Source: UniProtKB-KW
  • protein trimerization Source: UniProtKB
  • protein ubiquitination Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Immunity, Innate immunity, Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase TRIM4 (EC:6.3.2.-)
Alternative name(s):
RING finger protein 87
Tripartite motif-containing protein 4
Gene namesi
Name:TRIM4
Synonyms:RNF87
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:16275. TRIM4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • plasma membrane Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi27 – 271C → S: Abolishes ligase activity. 1 Publication

Organism-specific databases

PharmGKBiPA38108.

Polymorphism and mutation databases

BioMutaiTRIM4.
DMDMi209572691.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 500500E3 ubiquitin-protein ligase TRIM4PRO_0000056200Add
BLAST

Proteomic databases

MaxQBiQ9C037.
PaxDbiQ9C037.
PRIDEiQ9C037.

PTM databases

PhosphoSiteiQ9C037.

Expressioni

Gene expression databases

BgeeiQ9C037.
CleanExiHS_TRIM4.
ExpressionAtlasiQ9C037. baseline and differential.
GenevisibleiQ9C037. HS.

Organism-specific databases

HPAiHPA019356.
HPA029461.

Interactioni

Subunit structurei

Homotrimer.1 Publication

Protein-protein interaction databases

BioGridi124585. 6 interactions.
IntActiQ9C037. 2 interactions.
STRINGi9606.ENSP00000348216.

Structurei

3D structure databases

ProteinModelPortaliQ9C037.
SMRiQ9C037. Positions 5-276, 309-494.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini288 – 500213B30.2/SPRYPROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili212 – 25342Sequence AnalysisAdd
BLAST

Sequence similaritiesi

Belongs to the TRIM/RBCC family.Curated
Contains 1 B box-type zinc finger.PROSITE-ProRule annotation
Contains 1 B30.2/SPRY domain.PROSITE-ProRule annotation
Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri12 – 5342RING-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri82 – 12342B box-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Coiled coil, Zinc-finger

Phylogenomic databases

eggNOGiNOG322533.
GeneTreeiENSGT00760000118893.
HOGENOMiHOG000234133.
HOVERGENiHBG001357.
InParanoidiQ9C037.
KOiK11998.
OMAiCRGCLHR.
PhylomeDBiQ9C037.
TreeFamiTF338674.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
4.10.45.10. 1 hit.
InterProiIPR001870. B30.2/SPRY.
IPR003879. Butyrophylin.
IPR013320. ConA-like_dom.
IPR003877. SPRY_dom.
IPR000315. Znf_B-box.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PfamiPF00622. SPRY. 1 hit.
PF00643. zf-B_box. 1 hit.
[Graphical view]
PRINTSiPR01407. BUTYPHLNCDUF.
SMARTiSM00336. BBOX. 1 hit.
SM00184. RING. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.
PROSITEiPS50188. B302_SPRY. 1 hit.
PS50119. ZF_BBOX. 1 hit.
PS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

Isoform Alpha (identifier: Q9C037-1) [UniParc]FASTAAdd to basket

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
MEAEDIQEEL TCPICLDYFQ DPVSIECGHN FCRGCLHRNW APGGGPFPCP
60 70 80 90 100
ECRHPSAPAA LRPNWALARL TEKTQRRRLG PVPPGLCGRH WEPLRLFCED
110 120 130 140 150
DQRPVCLVCR ESQEHQTHAM APIDEAFESY RTGNFDIHVD EWKRRLIRLL
160 170 180 190 200
LYHFKQEEKL LKSQRNLVAK MKKVMHLQDV EVKNATQWKD KIKSQRMRIS
210 220 230 240 250
TEFSKLHNFL VEEEDLFLQR LNKEEEETKK KLNENTLKLN QTIASLKKLI
260 270 280 290 300
LEVGEKSQAP TLELLQNPKE VLTRSEIQDV NYSLEAVKVK TVCQIPLMKE
310 320 330 340 350
MLKRFQVAVN LAEDTAHPKL VFSQEGRYVK NTASASSWPV FSSAWNYFAG
360 370 380 390 400
WRNPQKTAFV ERFQHLPCVL GKNVFTSGKH YWEVESRDSL EVAVGVCRED
410 420 430 440 450
VMGITDRSKM SPDVGIWAIY WSAAGYWPLI GFPGTPTQQE PALHRVGVYL
460 470 480 490 500
DRGTGNVSFY SAVDGVHLHT FSCSSVSRLR PFFWLSPLAS LVIPPVTDRK
Length:500
Mass (Da):57,461
Last modified:October 14, 2008 - v2
Checksum:i427D7F3DBF53A72C
GO
Isoform Beta (identifier: Q9C037-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     132-157: Missing.

Show »
Length:474
Mass (Da):54,151
Checksum:iB8C2FB94B2E2183E
GO
Isoform Gamma (identifier: Q9C037-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     132-157: Missing.
     307-320: VAVNLAEDTAHPKL → ATKIKTQKQNRHNM
     321-500: Missing.

Show »
Length:294
Mass (Da):34,194
Checksum:i3E5F09926DD4A824
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti154 – 1541F → S in AAG53477 (PubMed:11331580).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti367 – 3671P → S.
Corresponds to variant rs35432946 [ dbSNP | Ensembl ].
VAR_046715
Natural varianti474 – 4741S → C.
Corresponds to variant rs33998596 [ dbSNP | Ensembl ].
VAR_046716

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei132 – 15726Missing in isoform Beta and isoform Gamma. 2 PublicationsVSP_010197Add
BLAST
Alternative sequencei307 – 32014VAVNL…AHPKL → ATKIKTQKQNRHNM in isoform Gamma. 1 PublicationVSP_010198Add
BLAST
Alternative sequencei321 – 500180Missing in isoform Gamma. 1 PublicationVSP_010199Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF220023 mRNA. Translation: AAG53477.1.
AF220024 mRNA. Translation: AAG53478.1.
AC011904 Genomic DNA. Translation: AAS07396.1.
AC011904 Genomic DNA. Translation: AAS07398.1.
AC011904 Genomic DNA. Translation: AAS07397.1.
CH236956 Genomic DNA. Translation: EAL23864.1.
CH471091 Genomic DNA. Translation: EAW76625.1.
CH471091 Genomic DNA. Translation: EAW76626.1.
CH236956 Genomic DNA. Translation: EAL23865.1.
BC011763 mRNA. Translation: AAH11763.1.
BC025949 mRNA. Translation: AAH25949.1.
CCDSiCCDS5678.1. [Q9C037-2]
CCDS5679.1. [Q9C037-1]
RefSeqiNP_148977.2. NM_033017.3. [Q9C037-1]
NP_149082.1. NM_033091.2. [Q9C037-2]
UniGeneiHs.50749.

Genome annotation databases

EnsembliENST00000349062; ENSP00000275736; ENSG00000146833. [Q9C037-2]
ENST00000354241; ENSP00000346186; ENSG00000146833. [Q9C037-3]
ENST00000355947; ENSP00000348216; ENSG00000146833.
GeneIDi89122.
KEGGihsa:89122.
UCSCiuc003usd.3. human. [Q9C037-1]
uc003use.3. human. [Q9C037-2]
uc003usf.3. human. [Q9C037-3]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF220023 mRNA. Translation: AAG53477.1.
AF220024 mRNA. Translation: AAG53478.1.
AC011904 Genomic DNA. Translation: AAS07396.1.
AC011904 Genomic DNA. Translation: AAS07398.1.
AC011904 Genomic DNA. Translation: AAS07397.1.
CH236956 Genomic DNA. Translation: EAL23864.1.
CH471091 Genomic DNA. Translation: EAW76625.1.
CH471091 Genomic DNA. Translation: EAW76626.1.
CH236956 Genomic DNA. Translation: EAL23865.1.
BC011763 mRNA. Translation: AAH11763.1.
BC025949 mRNA. Translation: AAH25949.1.
CCDSiCCDS5678.1. [Q9C037-2]
CCDS5679.1. [Q9C037-1]
RefSeqiNP_148977.2. NM_033017.3. [Q9C037-1]
NP_149082.1. NM_033091.2. [Q9C037-2]
UniGeneiHs.50749.

3D structure databases

ProteinModelPortaliQ9C037.
SMRiQ9C037. Positions 5-276, 309-494.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124585. 6 interactions.
IntActiQ9C037. 2 interactions.
STRINGi9606.ENSP00000348216.

PTM databases

PhosphoSiteiQ9C037.

Polymorphism and mutation databases

BioMutaiTRIM4.
DMDMi209572691.

Proteomic databases

MaxQBiQ9C037.
PaxDbiQ9C037.
PRIDEiQ9C037.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000349062; ENSP00000275736; ENSG00000146833. [Q9C037-2]
ENST00000354241; ENSP00000346186; ENSG00000146833. [Q9C037-3]
ENST00000355947; ENSP00000348216; ENSG00000146833.
GeneIDi89122.
KEGGihsa:89122.
UCSCiuc003usd.3. human. [Q9C037-1]
uc003use.3. human. [Q9C037-2]
uc003usf.3. human. [Q9C037-3]

Organism-specific databases

CTDi89122.
GeneCardsiGC07M099474.
HGNCiHGNC:16275. TRIM4.
HPAiHPA019356.
HPA029461.
neXtProtiNX_Q9C037.
PharmGKBiPA38108.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG322533.
GeneTreeiENSGT00760000118893.
HOGENOMiHOG000234133.
HOVERGENiHBG001357.
InParanoidiQ9C037.
KOiK11998.
OMAiCRGCLHR.
PhylomeDBiQ9C037.
TreeFamiTF338674.

Enzyme and pathway databases

UniPathwayiUPA00143.

Miscellaneous databases

ChiTaRSiTRIM4. human.
GenomeRNAii89122.
NextBioi76224.
PROiQ9C037.

Gene expression databases

BgeeiQ9C037.
CleanExiHS_TRIM4.
ExpressionAtlasiQ9C037. baseline and differential.
GenevisibleiQ9C037. HS.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
4.10.45.10. 1 hit.
InterProiIPR001870. B30.2/SPRY.
IPR003879. Butyrophylin.
IPR013320. ConA-like_dom.
IPR003877. SPRY_dom.
IPR000315. Znf_B-box.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PfamiPF00622. SPRY. 1 hit.
PF00643. zf-B_box. 1 hit.
[Graphical view]
PRINTSiPR01407. BUTYPHLNCDUF.
SMARTiSM00336. BBOX. 1 hit.
SM00184. RING. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.
PROSITEiPS50188. B302_SPRY. 1 hit.
PS50119. ZF_BBOX. 1 hit.
PS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS ALPHA AND BETA).
  2. "The DNA sequence of human chromosome 7."
    Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L.
    , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
    Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "Human chromosome 7: DNA sequence and biology."
    Scherer S.W., Cheung J., MacDonald J.R., Osborne L.R., Nakabayashi K., Herbrick J.-A., Carson A.R., Parker-Katiraee L., Skaug J., Khaja R., Zhang J., Hudek A.K., Li M., Haddad M., Duggan G.E., Fernandez B.A., Kanematsu E., Gentles S.
    , Christopoulos C.C., Choufani S., Kwasnicka D., Zheng X.H., Lai Z., Nusskern D.R., Zhang Q., Gu Z., Lu F., Zeesman S., Nowaczyk M.J., Teshima I., Chitayat D., Shuman C., Weksberg R., Zackai E.H., Grebe T.A., Cox S.R., Kirkpatrick S.J., Rahman N., Friedman J.M., Heng H.H.Q., Pelicci P.G., Lo-Coco F., Belloni E., Shaffer L.G., Pober B., Morton C.C., Gusella J.F., Bruns G.A.P., Korf B.R., Quade B.J., Ligon A.H., Ferguson H., Higgins A.W., Leach N.T., Herrick S.R., Lemyre E., Farra C.G., Kim H.-G., Summers A.M., Gripp K.W., Roberts W., Szatmari P., Winsor E.J.T., Grzeschik K.-H., Teebi A., Minassian B.A., Kere J., Armengol L., Pujana M.A., Estivill X., Wilson M.D., Koop B.F., Tosi S., Moore G.E., Boright A.P., Zlotorynski E., Kerem B., Kroisel P.M., Petek E., Oscier D.G., Mould S.J., Doehner H., Doehner K., Rommens J.M., Vincent J.B., Venter J.C., Li P.W., Mural R.J., Adams M.D., Tsui L.-C.
    Science 300:767-772(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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 GAMMA).
    Tissue: Melanoma.
  6. Cited for: SUBUNIT, SUBCELLULAR LOCATION.
  7. "TRIM4 modulates type I interferon induction and cellular antiviral response by targeting RIG-I for K63-linked ubiquitination."
    Yan J., Li Q., Mao A.P., Hu M.M., Shu H.B.
    J. Mol. Cell Biol. 6:154-163(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, PATHWAY, MUTAGENESIS OF CYS-27.

Entry informationi

Entry nameiTRIM4_HUMAN
AccessioniPrimary (citable) accession number: Q9C037
Secondary accession number(s): A4D298
, Q75MK1, Q96F06, Q9C036
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2004
Last sequence update: October 14, 2008
Last modified: July 22, 2015
This is version 121 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.