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Protein

Polyhomeotic-like protein 3

Gene

PHC3

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

Functioni

Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri776 – 810FCS-typePROSITE-ProRule annotationAdd BLAST35

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-2559580. Oxidative Stress Induced Senescence.
R-HSA-3108214. SUMOylation of DNA damage response and repair proteins.
R-HSA-4570464. SUMOylation of RNA binding proteins.

Names & Taxonomyi

Protein namesi
Recommended name:
Polyhomeotic-like protein 3
Alternative name(s):
Early development regulatory protein 3
Homolog of polyhomeotic 3
Short name:
hPH3
Gene namesi
Name:PHC3
Synonyms:EDR3, PH3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:15682. PHC3.

Subcellular locationi

GO - Cellular componenti

  • actin cytoskeleton Source: HPA
  • intracellular membrane-bounded organelle Source: HPA
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
  • PcG protein complex Source: UniProtKB
  • PRC1 complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi80012.
OpenTargetsiENSG00000173889.
PharmGKBiPA134886018.

Polymorphism and mutation databases

BioMutaiPHC3.
DMDMi74715388.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000762901 – 983Polyhomeotic-like protein 3Add BLAST983

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei263PhosphoserineCombined sources1
Modified residuei272PhosphoserineCombined sources1
Modified residuei315PhosphoserineCombined sources1
Modified residuei609PhosphothreonineCombined sources1
Modified residuei614PhosphothreonineCombined sources1
Modified residuei616PhosphoserineCombined sources1
Modified residuei761PhosphoserineCombined sources1
Modified residuei762PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ8NDX5.
PaxDbiQ8NDX5.
PeptideAtlasiQ8NDX5.
PRIDEiQ8NDX5.

PTM databases

iPTMnetiQ8NDX5.
PhosphoSitePlusiQ8NDX5.

Expressioni

Gene expression databases

BgeeiENSG00000173889.
CleanExiHS_PHC3.
ExpressionAtlasiQ8NDX5. baseline and differential.
GenevisibleiQ8NDX5. HS.

Organism-specific databases

HPAiHPA039162.
HPA062031.

Interactioni

Subunit structurei

Component of a PRC1-like complex.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
OGTO152943EBI-1223801,EBI-539828

Protein-protein interaction databases

BioGridi123068. 25 interactors.
IntActiQ8NDX5. 26 interactors.
MINTiMINT-5005444.
STRINGi9606.ENSP00000420294.

Structurei

Secondary structure

1983
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi916 – 918Combined sources3
Helixi921 – 929Combined sources9
Helixi935 – 943Combined sources9
Helixi948 – 952Combined sources5
Helixi956 – 959Combined sources4
Turni960 – 962Combined sources3
Helixi967 – 982Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4PZNX-ray2.30A/B/C/D/E914-983[»]
4PZOX-ray2.25A/B/C/D/E/F914-983[»]
ProteinModelPortaliQ8NDX5.
SMRiQ8NDX5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini919 – 983SAMPROSITE-ProRule annotationAdd BLAST65

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi691 – 720HD1Add BLAST30

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi19 – 26Poly-Thr8
Compositional biasi89 – 287Ser-richAdd BLAST199
Compositional biasi324 – 539Gln-richAdd BLAST216
Compositional biasi346 – 670Pro-richAdd BLAST325

Sequence similaritiesi

Contains 1 FCS-type zinc finger.PROSITE-ProRule annotation
Contains 1 SAM (sterile alpha motif) domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri776 – 810FCS-typePROSITE-ProRule annotationAdd BLAST35

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiENOG410IDZN. Eukaryota.
ENOG4111F0Y. LUCA.
GeneTreeiENSGT00550000074459.
HOVERGENiHBG106650.
InParanoidiQ8NDX5.
KOiK11458.
OMAiEMVQPEV.
OrthoDBiEOG091G02VS.
PhylomeDBiQ8NDX5.
TreeFamiTF331299.

Family and domain databases

Gene3Di1.10.150.50. 1 hit.
InterProiIPR001660. SAM.
IPR013761. SAM/pointed.
IPR012313. Znf_FCS.
[Graphical view]
PfamiPF00536. SAM_1. 1 hit.
[Graphical view]
SMARTiSM00454. SAM. 1 hit.
[Graphical view]
SUPFAMiSSF47769. SSF47769. 1 hit.
PROSITEiPS50105. SAM_DOMAIN. 1 hit.
PS51024. ZF_FCS. 1 hit.
[Graphical view]

Sequences (7)i

Sequence statusi: Complete.

This entry describes 7 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8NDX5-1) [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
MDTEPNPGTS SVSTTTSSTT TTTITTSSSR MQQPQISVYS GSDRHAVQVI
60 70 80 90 100
QQALHRPPSS AAQYLQQMYA AQQQHLMLHT AALQQQHLSS SQLQSLAAVQ
110 120 130 140 150
ASLSSGRPST SPTGSVTQQS SMSQTSINLS TSPTPAQLIS RSQASSSTSG
160 170 180 190 200
SITQQTMLLG STSPTLTASQ AQMYLRAQML IFTPATTVAA VQSDIPVVSS
210 220 230 240 250
SSSSSCQSAA TQVQNLTLRS QKLGVLSSSQ NGPPKSTSQT QSLTICHNKT
260 270 280 290 300
TVTSSKISQR DPSPESNKKG ESPSLESRST AVTRTSSIHQ LIAPASYSPI
310 320 330 340 350
QPHSLIKHQQ IPLHSPPSKV SHHQLILQQQ QQQIQPITLQ NSTQDPPPSQ
360 370 380 390 400
HCIPLQNHGL PPAPSNAQSQ HCSPIQSHPS PLTVSPNQSQ SAQQSVVVSP
410 420 430 440 450
PPPHSPSQSP TIIIHPQALI QPHPLVSSAL QPGPNLQQST ANQVQATAQL
460 470 480 490 500
NLPSHLPLPA SPVVHIGPVQ QSALVSPGQQ IVSPSHQQYS SLQSSPIPIA
510 520 530 540 550
SPPQMSTSPP AQIPPLPLQS MQSLQVQPEI LSQGQVLVQN ALVSEEELPA
560 570 580 590 600
AEALVQLPFQ TLPPPQTVAV NLQVQPPAPV DPPVVYQVED VCEEEMPEES
610 620 630 640 650
DECVRMDRTP PPPTLSPAAI TVGRGEDLTS EHPLLEQVEL PAVASVSASV
660 670 680 690 700
IKSPSDPSHV SVPPPPLLLP AATTRSNSTS MHSSIPSIEN KPPQAIVKPQ
710 720 730 740 750
ILTHVIEGFV IQEGLEPFPV SRSSLLIEQP VKKRPLLDNQ VINSVCVQPE
760 770 780 790 800
LQNNTKHADN SSDTEMEDMI AEETLEEMDS ELLKCEFCGK MGYANEFLRS
810 820 830 840 850
KRFCTMSCAK RYNVSCSKKF ALSRWNRKPD NQSLGHRGRR PSGPDGAARE
860 870 880 890 900
HILRQLPITY PSAEEDLASH EDSVPSAMTT RLRRQSERER ERELRDVRIR
910 920 930 940 950
KMPENSDLLP VAQTEPSIWT VDDVWAFIHS LPGCQDIADE FRAQEIDGQA
960 970 980
LLLLKEDHLM SAMNIKLGPA LKICARINSL KES
Length:983
Mass (Da):106,162
Last modified:October 1, 2002 - v1
Checksum:i05819632A1675049
GO
Isoform 2 (identifier: Q8NDX5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     123-141: Missing.

Show »
Length:964
Mass (Da):104,178
Checksum:iEE515D7DDFB53E7B
GO
Isoform 3 (identifier: Q8NDX5-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MAEAEFKDHSTAM
     295-321: ASYSPIQPHSLIKHQQIPLHSPPSKVS → GGIKLLLKIVVLFIFLADRAKQRMFMT
     322-983: Missing.

Note: No experimental confirmation available.
Show »
Length:333
Mass (Da):35,253
Checksum:iF599992070F91F88
GO
Isoform 4 (identifier: Q8NDX5-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     48-51: Missing.
     180-190: LIFTPATTVAA → VRYELPNFFSV
     191-983: Missing.

Show »
Length:186
Mass (Da):19,748
Checksum:i351B7AD420AA40B7
GO
Isoform 5 (identifier: Q8NDX5-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MAEAEFKDHSTAM
     127-139: INLSTSPTPAQLI → VSSLNFFFLDLKF
     140-983: Missing.

Show »
Length:151
Mass (Da):16,228
Checksum:iB0837669A1311637
GO
Isoform 6 (identifier: Q8NDX5-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     48-51: Missing.
     127-139: INLSTSPTPAQLI → VSSLNFFFLDLKF
     140-983: Missing.

Note: No experimental confirmation available.
Show »
Length:135
Mass (Da):14,441
Checksum:iEA82C7776AA961A5
GO
Isoform 7 (identifier: Q8NDX5-7) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MAEAEFKDHSTAM

Show »
Length:995
Mass (Da):107,480
Checksum:iD3A424246ADC139A
GO

Sequence cautioni

Isoform 5 : The sequence BAB14245 differs from that shown. Reason: Frameshift at position 147.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti50I → F in AAM46139 (Ref. 3) Curated1
Sequence conflicti53A → S in AAM51781 (PubMed:12167701).Curated1
Sequence conflicti310Q → R in EF560717 (PubMed:17974005).Curated1
Sequence conflicti435N → D in EF560717 (PubMed:17974005).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0167631M → MAEAEFKDHSTAM in isoform 3, isoform 5 and isoform 7. 3 Publications1
Alternative sequenceiVSP_01676448 – 51Missing in isoform 4 and isoform 6. 2 Publications4
Alternative sequenceiVSP_016765123 – 141Missing in isoform 2. 1 PublicationAdd BLAST19
Alternative sequenceiVSP_016766127 – 139INLST…PAQLI → VSSLNFFFLDLKF in isoform 5 and isoform 6. 2 PublicationsAdd BLAST13
Alternative sequenceiVSP_016767140 – 983Missing in isoform 5 and isoform 6. 2 PublicationsAdd BLAST844
Alternative sequenceiVSP_016768180 – 190LIFTPATTVAA → VRYELPNFFSV in isoform 4. 1 PublicationAdd BLAST11
Alternative sequenceiVSP_016769191 – 983Missing in isoform 4. 1 PublicationAdd BLAST793
Alternative sequenceiVSP_016770295 – 321ASYSP…PSKVS → GGIKLLLKIVVLFIFLADRA KQRMFMT in isoform 3. 1 PublicationAdd BLAST27
Alternative sequenceiVSP_016771322 – 983Missing in isoform 3. 1 PublicationAdd BLAST662

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ320486 mRNA. Translation: CAC86587.2.
AF444193 mRNA. Translation: AAM51781.1.
AF380154 mRNA. Translation: AAM46139.1.
AK022791 mRNA. Translation: BAB14245.1. Frameshift.
AK023029 mRNA. Translation: BAB14365.1.
BX647868 mRNA. Translation: CAI46090.1.
EF560717 mRNA. No translation available.
AC008040 Genomic DNA. No translation available.
AC023891 Genomic DNA. No translation available.
CH471052 Genomic DNA. Translation: EAW78519.1.
BC022325 mRNA. Translation: AAH22325.1.
BC070164 mRNA. Translation: AAH70164.1.
BC131772 mRNA. Translation: AAI31773.1.
CCDSiCCDS46952.1. [Q8NDX5-7]
CCDS77858.1. [Q8NDX5-1]
RefSeqiNP_001295045.1. NM_001308116.1. [Q8NDX5-1]
NP_079223.3. NM_024947.3. [Q8NDX5-7]
UniGeneiHs.529592.
Hs.694467.

Genome annotation databases

EnsembliENST00000494943; ENSP00000420271; ENSG00000173889. [Q8NDX5-1]
ENST00000495893; ENSP00000420294; ENSG00000173889. [Q8NDX5-7]
ENST00000497658; ENSP00000420454; ENSG00000173889. [Q8NDX5-5]
GeneIDi80012.
KEGGihsa:80012.
UCSCiuc003fgl.3. human. [Q8NDX5-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ320486 mRNA. Translation: CAC86587.2.
AF444193 mRNA. Translation: AAM51781.1.
AF380154 mRNA. Translation: AAM46139.1.
AK022791 mRNA. Translation: BAB14245.1. Frameshift.
AK023029 mRNA. Translation: BAB14365.1.
BX647868 mRNA. Translation: CAI46090.1.
EF560717 mRNA. No translation available.
AC008040 Genomic DNA. No translation available.
AC023891 Genomic DNA. No translation available.
CH471052 Genomic DNA. Translation: EAW78519.1.
BC022325 mRNA. Translation: AAH22325.1.
BC070164 mRNA. Translation: AAH70164.1.
BC131772 mRNA. Translation: AAI31773.1.
CCDSiCCDS46952.1. [Q8NDX5-7]
CCDS77858.1. [Q8NDX5-1]
RefSeqiNP_001295045.1. NM_001308116.1. [Q8NDX5-1]
NP_079223.3. NM_024947.3. [Q8NDX5-7]
UniGeneiHs.529592.
Hs.694467.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4PZNX-ray2.30A/B/C/D/E914-983[»]
4PZOX-ray2.25A/B/C/D/E/F914-983[»]
ProteinModelPortaliQ8NDX5.
SMRiQ8NDX5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123068. 25 interactors.
IntActiQ8NDX5. 26 interactors.
MINTiMINT-5005444.
STRINGi9606.ENSP00000420294.

PTM databases

iPTMnetiQ8NDX5.
PhosphoSitePlusiQ8NDX5.

Polymorphism and mutation databases

BioMutaiPHC3.
DMDMi74715388.

Proteomic databases

MaxQBiQ8NDX5.
PaxDbiQ8NDX5.
PeptideAtlasiQ8NDX5.
PRIDEiQ8NDX5.

Protocols and materials databases

DNASUi80012.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000494943; ENSP00000420271; ENSG00000173889. [Q8NDX5-1]
ENST00000495893; ENSP00000420294; ENSG00000173889. [Q8NDX5-7]
ENST00000497658; ENSP00000420454; ENSG00000173889. [Q8NDX5-5]
GeneIDi80012.
KEGGihsa:80012.
UCSCiuc003fgl.3. human. [Q8NDX5-1]

Organism-specific databases

CTDi80012.
DisGeNETi80012.
GeneCardsiPHC3.
H-InvDBHIX0023090.
HGNCiHGNC:15682. PHC3.
HPAiHPA039162.
HPA062031.
neXtProtiNX_Q8NDX5.
OpenTargetsiENSG00000173889.
PharmGKBiPA134886018.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IDZN. Eukaryota.
ENOG4111F0Y. LUCA.
GeneTreeiENSGT00550000074459.
HOVERGENiHBG106650.
InParanoidiQ8NDX5.
KOiK11458.
OMAiEMVQPEV.
OrthoDBiEOG091G02VS.
PhylomeDBiQ8NDX5.
TreeFamiTF331299.

Enzyme and pathway databases

ReactomeiR-HSA-2559580. Oxidative Stress Induced Senescence.
R-HSA-3108214. SUMOylation of DNA damage response and repair proteins.
R-HSA-4570464. SUMOylation of RNA binding proteins.

Miscellaneous databases

ChiTaRSiPHC3. human.
GeneWikiiPHC3.
GenomeRNAii80012.
PROiQ8NDX5.

Gene expression databases

BgeeiENSG00000173889.
CleanExiHS_PHC3.
ExpressionAtlasiQ8NDX5. baseline and differential.
GenevisibleiQ8NDX5. HS.

Family and domain databases

Gene3Di1.10.150.50. 1 hit.
InterProiIPR001660. SAM.
IPR013761. SAM/pointed.
IPR012313. Znf_FCS.
[Graphical view]
PfamiPF00536. SAM_1. 1 hit.
[Graphical view]
SMARTiSM00454. SAM. 1 hit.
[Graphical view]
SUPFAMiSSF47769. SSF47769. 1 hit.
PROSITEiPS50105. SAM_DOMAIN. 1 hit.
PS51024. ZF_FCS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPHC3_HUMAN
AccessioniPrimary (citable) accession number: Q8NDX5
Secondary accession number(s): A2RRP9
, Q5HYF0, Q6NSG2, Q8NFT7, Q8NFZ1, Q8TBM2, Q9H971, Q9H9I4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: October 1, 2002
Last modified: November 30, 2016
This is version 129 of the entry and version 1 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

Miscellaneous

The hPRC-H complex purification reported by PubMed:12167701 probably presents a mixture of different PRC1-like complexes.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.