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Protein

Zinc fingers and homeoboxes protein 3

Gene

ZHX3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Repressor
Biological processDifferentiation, Transcription, Transcription regulation
LigandMetal-binding, Zinc

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

EuPathDBiHostDB:ENSG00000174306.21
HGNCiHGNC:15935 ZHX3
MIMi609598 gene
neXtProtiNX_Q9H4I2

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
ProteomicsDBi80842

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 Expressed in 221 organ(s), highest expression level in corpus callosum
CleanExiHS_ZHX3
ExpressionAtlasiQ9H4I2 baseline and differential
GenevisibleiQ9H4I2 HS

Organism-specific databases

HPAiHPA046498

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-protein interaction databases

BioGridi116688, 10 interactors
IntActiQ9H4I2, 5 interactors
MINTiQ9H4I2
STRINGi9606.ENSP00000362360

Structurei

Secondary structure

1956
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

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
OMAiKGSRAMM
OrthoDBiEOG091G02WT
PhylomeDBiQ9H4I2
TreeFamiTF333363

Family and domain databases

CDDicd00086 homeodomain, 4 hits
InterProiView protein in InterPro
IPR009057 Homeobox-like_sf
IPR001356 Homeobox_dom
IPR024578 Homez_homeobox_dom
IPR036236 Znf_C2H2_sf
IPR013087 Znf_C2H2_type
PfamiView protein in Pfam
PF00046 Homeobox, 3 hits
PF11569 Homez, 1 hit
SMARTiView protein in SMART
SM00389 HOX, 4 hits
SM00355 ZnF_C2H2, 2 hits
SUPFAMiSSF46689 SSF46689, 5 hits
SSF57667 SSF57667, 1 hit
PROSITEiView protein in PROSITE
PS50071 HOMEOBOX_2, 4 hits

Sequences (2+)i

Sequence statusi: Complete.

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

This entry has 2 described isoforms and 8 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 8 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0Y6F5H0Y6F5_HUMAN
Zinc fingers and homeoboxes protein...
ZHX3
678Annotation score:
H0YNY7H0YNY7_HUMAN
Zinc fingers and homeoboxes protein...
ZHX3
315Annotation score:
F6XGA7F6XGA7_HUMAN
Zinc fingers and homeoboxes protein...
ZHX3
118Annotation score:
H0YLR4H0YLR4_HUMAN
Zinc fingers and homeoboxes protein...
ZHX3
127Annotation score:
F6UQN6F6UQN6_HUMAN
Zinc fingers and homeoboxes protein...
ZHX3
96Annotation score:
F6UBH9F6UBH9_HUMAN
Zinc fingers and homeoboxes protein...
ZHX3
46Annotation score:
A0A0A0MSU5A0A0A0MSU5_HUMAN
Zinc fingers and homeoboxes protein...
ZHX3
89Annotation score:
A0A0A0MST6A0A0A0MST6_HUMAN
Zinc fingers and homeoboxes protein...
ZHX3
47Annotation score:

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 dbSNP:rs17265513Ensembl.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 No translation available.
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
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

Similar proteinsi

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 No translation available.
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
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
MINTiQ9H4I2
STRINGi9606.ENSP00000362360

PTM databases

iPTMnetiQ9H4I2
PhosphoSitePlusiQ9H4I2

Polymorphism and mutation databases

BioMutaiZHX3
DMDMi44889075

Proteomic databases

EPDiQ9H4I2
MaxQBiQ9H4I2
PaxDbiQ9H4I2
PeptideAtlasiQ9H4I2
PRIDEiQ9H4I2
ProteomicsDBi80842

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
EuPathDBiHostDB:ENSG00000174306.21
GeneCardsiZHX3
H-InvDBiHIX0015822
HGNCiHGNC:15935 ZHX3
HPAiHPA046498
MIMi609598 gene
neXtProtiNX_Q9H4I2
OpenTargetsiENSG00000174306
PharmGKBiPA38056
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

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

Miscellaneous databases

ChiTaRSiZHX3 human
EvolutionaryTraceiQ9H4I2
GeneWikiiZHX3
GenomeRNAii23051
PROiPR:Q9H4I2
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000174306 Expressed in 221 organ(s), highest expression level in corpus callosum
CleanExiHS_ZHX3
ExpressionAtlasiQ9H4I2 baseline and differential
GenevisibleiQ9H4I2 HS

Family and domain databases

CDDicd00086 homeodomain, 4 hits
InterProiView protein in InterPro
IPR009057 Homeobox-like_sf
IPR001356 Homeobox_dom
IPR024578 Homez_homeobox_dom
IPR036236 Znf_C2H2_sf
IPR013087 Znf_C2H2_type
PfamiView protein in Pfam
PF00046 Homeobox, 3 hits
PF11569 Homez, 1 hit
SMARTiView protein in SMART
SM00389 HOX, 4 hits
SM00355 ZnF_C2H2, 2 hits
SUPFAMiSSF46689 SSF46689, 5 hits
SSF57667 SSF57667, 1 hit
PROSITEiView protein in PROSITE
PS50071 HOMEOBOX_2, 4 hits
ProtoNetiSearch...

Entry informationi

Entry nameiZHX3_HUMAN
AccessioniPrimary (citable) accession number: Q9H4I2
Secondary accession number(s): E1P5W5
, F5H820, O43145, Q6NUJ7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 10, 2002
Last sequence update: March 1, 2004
Last modified: November 7, 2018
This is version 163 of the entry and version 3 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  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. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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