Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Zinc fingers and homeoboxes protein 3

Gene

ZHX3

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

Functioni

Acts as a transcriptional repressor. Involved in the early stages of mesenchymal stem cell (MSC) osteogenic differentiation. Is a regulator of podocyte gene expression during primary glomerula disease. Binds to promoter DNA.2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri77 – 100C2H2-type 1Add BLAST24
Zinc fingeri109 – 132C2H2-type 2Add BLAST24
DNA bindingi304 – 363Homeobox 1PROSITE-ProRule annotationAdd BLAST60
DNA bindingi494 – 553Homeobox 2PROSITE-ProRule annotationAdd BLAST60
DNA bindingi612 – 671Homeobox 3PROSITE-ProRule annotationAdd BLAST60
DNA bindingi764 – 823Homeobox 4PROSITE-ProRule annotationAdd BLAST60
DNA bindingi835 – 894Homeobox 5PROSITE-ProRule annotationAdd BLAST60

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • protein heterodimerization activity Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB
  • transcription corepressor activity Source: GO_Central
  • transcription factor activity, sequence-specific DNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Differentiation, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000174306-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Zinc fingers and homeoboxes protein 3
Alternative name(s):
Triple homeobox protein 1
Zinc finger and homeodomain protein 3
Gene namesi
Name:ZHX3
Synonyms:KIAA0395, TIX1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:15935. ZHX3.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation1 Publication

GO - Cellular componenti

  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000174306.
PharmGKBiPA38056.

Polymorphism and mutation databases

BioMutaiZHX3.
DMDMi44889075.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000493951 – 956Zinc fingers and homeoboxes protein 3Add BLAST956

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei599PhosphoserineCombined sources1
Modified residuei604PhosphoserineCombined sources1
Modified residuei680PhosphoserineCombined sources1
Modified residuei708PhosphoserineBy similarity1
Modified residuei723PhosphoserineCombined sources1
Modified residuei927PhosphoserineCombined sources1
Modified residuei946PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9H4I2.
MaxQBiQ9H4I2.
PaxDbiQ9H4I2.
PeptideAtlasiQ9H4I2.
PRIDEiQ9H4I2.

PTM databases

iPTMnetiQ9H4I2.
PhosphoSitePlusiQ9H4I2.

Expressioni

Tissue specificityi

Widely expressed. High expression in kidney. Expressed during osteogenic differentiation.2 Publications

Inductioni

Up-regulated during osteogenic differentiation of mesenchymal stem cells.1 Publication

Gene expression databases

BgeeiENSG00000174306.
CleanExiHS_ZHX3.
ExpressionAtlasiQ9H4I2. baseline and differential.
GenevisibleiQ9H4I2. HS.

Organism-specific databases

HPAiHPA006687.
HPA046498.

Interactioni

Subunit structurei

Homodimer (via homeobox domain). Also forms heterodimers with ZHX1 and ZHX2. Heterodimerization with ZHX1 is a prerequisite for repressor activity. Interacts with NFYA.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
NLKQ9UBE84EBI-948582,EBI-366978

GO - Molecular functioni

  • protein heterodimerization activity Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi116688. 10 interactors.
IntActiQ9H4I2. 5 interactors.
MINTiMINT-2870187.
STRINGi9606.ENSP00000362360.

Structurei

Secondary structure

1956
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi503 – 51513
Beta strandi516 – 5183
Helixi522 – 53110
Helixi535 – 54814
Beta strandi549 – 5513
Beta strandi554 – 5563
Helixi621 – 63313
Helixi639 – 64911
Helixi653 – 66311
Helixi666 – 6694

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DA5NMR-A613-674[»]
2DN0NMR-A494-556[»]
ProteinModelPortaliQ9H4I2.
SMRiQ9H4I2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H4I2.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 107Required for nuclear localizationAdd BLAST107
Regioni242 – 488Required for homodimerization and interaction with NFYA1 PublicationAdd BLAST247
Regioni303 – 502Required for repressor activityAdd BLAST200
Regioni497 – 555Required for nuclear localizationAdd BLAST59

Sequence similaritiesi

Belongs to the ZHX family.Curated
Contains 2 C2H2-type zinc fingers.Curated
Contains 5 homeobox DNA-binding domains.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri77 – 100C2H2-type 1Add BLAST24
Zinc fingeri109 – 132C2H2-type 2Add BLAST24

Keywords - Domaini

Homeobox, Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG410IHET. Eukaryota.
ENOG410Z8A2. LUCA.
GeneTreeiENSGT00530000063149.
HOGENOMiHOG000013231.
HOVERGENiHBG007920.
InParanoidiQ9H4I2.
OrthoDBiEOG091G02WT.
PhylomeDBiQ9H4I2.
TreeFamiTF333363.

Family and domain databases

Gene3Di1.10.10.60. 5 hits.
InterProiIPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR024578. Homez_dom.
IPR015880. Znf_C2H2-like.
[Graphical view]
PfamiPF00046. Homeobox. 3 hits.
PF11569. Homez. 1 hit.
[Graphical view]
SMARTiSM00389. HOX. 4 hits.
SM00355. ZnF_C2H2. 2 hits.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 5 hits.
PROSITEiPS50071. HOMEOBOX_2. 4 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9H4I2-1) [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
MASKRKSTTP CMIPVKTVVL QDASMEAQPA ETLPEGPQQD LPPEASAASS
60 70 80 90 100
EAAQNPSSTD GSTLANGHRS TLDGYLYSCK YCDFRSHDMT QFVGHMNSEH
110 120 130 140 150
TDFNKDPTFV CSGCSFLAKT PEGLSLHNAT CHSGEASFVW NVAKPDNHVV
160 170 180 190 200
VEQSIPESTS TPDLAGEPSA EGADGQAEII ITKTPIMKIM KGKAEAKKIH
210 220 230 240 250
TLKENVPSQP VGEALPKLST GEMEVREGDH SFINGAVPVS QASASSAKNP
260 270 280 290 300
HAANGPLIGT VPVLPAGIAQ FLSLQQQPPV HAQHHVHQPL PTAKALPKVM
310 320 330 340 350
IPLSSIPTYN AAMDSNSFLK NSFHKFPYPT KAELCYLTVV TKYPEEQLKI
360 370 380 390 400
WFTAQRLKQG ISWSPEEIED ARKKMFNTVI QSVPQPTITV LNTPLVASAG
410 420 430 440 450
NVQHLIQAAL PGHVVGQPEG TGGGLLVTQP LMANGLQATS SPLPLTVTSV
460 470 480 490 500
PKQPGVAPIN TVCSNTTSAV KVVNAAQSLL TACPSITSQA FLDASIYKNK
510 520 530 540 550
KSHEQLSALK GSFCRNQFPG QSEVEHLTKV TGLSTREVRK WFSDRRYHCR
560 570 580 590 600
NLKGSRAMIP GDHSSIIIDS VPEVSFSPSS KVPEVTCIPT TATLATHPSA
610 620 630 640 650
KRQSWHQTPD FTPTKYKERA PEQLRALESS FAQNPLPLDE ELDRLRSETK
660 670 680 690 700
MTRREIDSWF SERRKKVNAE ETKKAEENAS QEEEEAAEDE GGEEDLASEL
710 720 730 740 750
RVSGENGSLE MPSSHILAER KVSPIKINLK NLRVTEANGR NEIPGLGACD
760 770 780 790 800
PEDDESNKLA EQLPGKVSCK KTAQQRHLLR QLFVQTQWPS NQDYDSIMAQ
810 820 830 840 850
TGLPRPEVVR WFGDSRYALK NGQLKWYEDY KRGNFPPGLL VIAPGNRELL
860 870 880 890 900
QDYYMTHKML YEEDLQNLCD KTQMSSQQVK QWFAEKMGEE TRAVADTGSE
910 920 930 940 950
DQGPGTGELT AVHKGMGDTY SEVSENSESW EPRVPEASSE PFDTSSPQAG

RQLETD
Length:956
Mass (Da):104,658
Last modified:March 1, 2004 - v3
Checksum:iB3DB35CFC1781A3A
GO
Isoform 2 (identifier: Q9H4I2-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     879-956: VKQWFAEKMG...PQAGRQLETD → KQTEFDLINV...CRTFPLPSNG

Note: No experimental confirmation available.
Show »
Length:969
Mass (Da):106,318
Checksum:i22010A170A8BC89E
GO

Sequence cautioni

The sequence BAA23691 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti642L → M in AAH68569 (PubMed:15489334).Curated1
Sequence conflicti907G → T in BAA23691 (PubMed:9455477).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_049597310N → S.Corresponds to variant rs17265513dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_054307879 – 956VKQWF…QLETD → KQTEFDLINVKDWPVWETAC HVEEPNPTLCCHMPFPCPAA GHLGELPESSQTAQSLPLPS ACPPPSKQQARWGSHQFFLP QCRTFPLPSNG in isoform 2. 1 PublicationAdd BLAST78

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB081948 mRNA. Translation: BAC65211.1.
AB007855 mRNA. Translation: BAA23691.3. Different initiation.
AL022394 Genomic DNA. Translation: CAA18538.1.
AL031257 Genomic DNA. No translation available.
CH471077 Genomic DNA. Translation: EAW75987.1.
CH471077 Genomic DNA. Translation: EAW75988.1.
BC068569 mRNA. Translation: AAH68569.1.
CCDSiCCDS13315.1. [Q9H4I2-1]
RefSeqiNP_055850.1. NM_015035.3. [Q9H4I2-1]
XP_005260398.1. XM_005260341.3. [Q9H4I2-2]
XP_011527022.1. XM_011528720.1. [Q9H4I2-1]
XP_016883226.1. XM_017027737.1. [Q9H4I2-1]
XP_016883227.1. XM_017027738.1. [Q9H4I2-1]
UniGeneiHs.380133.

Genome annotation databases

EnsembliENST00000309060; ENSP00000312222; ENSG00000174306. [Q9H4I2-1]
ENST00000432768; ENSP00000415498; ENSG00000174306. [Q9H4I2-1]
ENST00000544979; ENSP00000443783; ENSG00000174306. [Q9H4I2-2]
ENST00000559234; ENSP00000452965; ENSG00000174306. [Q9H4I2-1]
ENST00000560361; ENSP00000454006; ENSG00000174306. [Q9H4I2-1]
GeneIDi23051.
KEGGihsa:23051.
UCSCiuc002xjr.2. human. [Q9H4I2-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB081948 mRNA. Translation: BAC65211.1.
AB007855 mRNA. Translation: BAA23691.3. Different initiation.
AL022394 Genomic DNA. Translation: CAA18538.1.
AL031257 Genomic DNA. No translation available.
CH471077 Genomic DNA. Translation: EAW75987.1.
CH471077 Genomic DNA. Translation: EAW75988.1.
BC068569 mRNA. Translation: AAH68569.1.
CCDSiCCDS13315.1. [Q9H4I2-1]
RefSeqiNP_055850.1. NM_015035.3. [Q9H4I2-1]
XP_005260398.1. XM_005260341.3. [Q9H4I2-2]
XP_011527022.1. XM_011528720.1. [Q9H4I2-1]
XP_016883226.1. XM_017027737.1. [Q9H4I2-1]
XP_016883227.1. XM_017027738.1. [Q9H4I2-1]
UniGeneiHs.380133.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DA5NMR-A613-674[»]
2DN0NMR-A494-556[»]
ProteinModelPortaliQ9H4I2.
SMRiQ9H4I2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116688. 10 interactors.
IntActiQ9H4I2. 5 interactors.
MINTiMINT-2870187.
STRINGi9606.ENSP00000362360.

PTM databases

iPTMnetiQ9H4I2.
PhosphoSitePlusiQ9H4I2.

Polymorphism and mutation databases

BioMutaiZHX3.
DMDMi44889075.

Proteomic databases

EPDiQ9H4I2.
MaxQBiQ9H4I2.
PaxDbiQ9H4I2.
PeptideAtlasiQ9H4I2.
PRIDEiQ9H4I2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000309060; ENSP00000312222; ENSG00000174306. [Q9H4I2-1]
ENST00000432768; ENSP00000415498; ENSG00000174306. [Q9H4I2-1]
ENST00000544979; ENSP00000443783; ENSG00000174306. [Q9H4I2-2]
ENST00000559234; ENSP00000452965; ENSG00000174306. [Q9H4I2-1]
ENST00000560361; ENSP00000454006; ENSG00000174306. [Q9H4I2-1]
GeneIDi23051.
KEGGihsa:23051.
UCSCiuc002xjr.2. human. [Q9H4I2-1]

Organism-specific databases

CTDi23051.
GeneCardsiZHX3.
H-InvDBHIX0015822.
HGNCiHGNC:15935. ZHX3.
HPAiHPA006687.
HPA046498.
MIMi609598. gene.
neXtProtiNX_Q9H4I2.
OpenTargetsiENSG00000174306.
PharmGKBiPA38056.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IHET. Eukaryota.
ENOG410Z8A2. LUCA.
GeneTreeiENSGT00530000063149.
HOGENOMiHOG000013231.
HOVERGENiHBG007920.
InParanoidiQ9H4I2.
OrthoDBiEOG091G02WT.
PhylomeDBiQ9H4I2.
TreeFamiTF333363.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000174306-MONOMER.

Miscellaneous databases

ChiTaRSiZHX3. human.
EvolutionaryTraceiQ9H4I2.
GeneWikiiZHX3.
GenomeRNAii23051.
PROiQ9H4I2.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000174306.
CleanExiHS_ZHX3.
ExpressionAtlasiQ9H4I2. baseline and differential.
GenevisibleiQ9H4I2. HS.

Family and domain databases

Gene3Di1.10.10.60. 5 hits.
InterProiIPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR024578. Homez_dom.
IPR015880. Znf_C2H2-like.
[Graphical view]
PfamiPF00046. Homeobox. 3 hits.
PF11569. Homez. 1 hit.
[Graphical view]
SMARTiSM00389. HOX. 4 hits.
SM00355. ZnF_C2H2. 2 hits.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 5 hits.
PROSITEiPS50071. HOMEOBOX_2. 4 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiZHX3_HUMAN
AccessioniPrimary (citable) accession number: Q9H4I2
Secondary accession number(s): E1P5W5
, F5H820, O43145, Q6NUJ7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2002
Last sequence update: March 1, 2004
Last modified: November 2, 2016
This is version 148 of the entry and version 3 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 20
    Human chromosome 20: 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.