2RVN

Solution structure of the chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Chromo domain-like	8063005	3000161	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Chromo	e2rvnA1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00385	Chromo (CHRromatin Organisation MOdifier) domain (Chromo)	Chromo (CHRromatin Organisation MOdifier) domain	-	Domain
B	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Chromobox protein homolog 5	histone deacetylase binding protein binding binding enzyme binding protein-containing complex binding chromatin binding ribonucleoprotein complex binding protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding DNA-binding transcription factor binding methylated histone binding modification-dependent protein binding histone binding histone deacetylase binding protein binding binding enzyme binding protein-containing complex binding chromatin binding ribonucleoprotein complex binding protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding DNA-binding transcription factor binding methylated histone binding modification-dependent protein binding histone binding methylation-dependent protein binding identical protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex histone methyltransferase complex catalytic complex nuclear protein-containing complex transferase complex nucleoplasm methyltransferase complex pericentric heterochromatin protein-DNA complex chromatin chromosome heterochromatin chromosomal region chromosome, centromeric region kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome chromocenter histone deacetylase complex transcription regulator complex transcription repressor complex ribonucleoprotein complex chromosome, telomeric region site of DNA damage nuclear body PML body
B	18-mer peptide of Histone H3	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development cellular developmental process ossification cell differentiation cellular process osteoblast differentiation spermatogenesis sexual reproduction multicellular organismal reproductive process male gamete generation gamete generation oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation germ cell development cell population proliferation regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process pericentric heterochromatin formation regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process fertilization single fertilization regulation of cellular component organization regulation of centromere complex assembly chromosome organization protein-DNA complex assembly regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization cellular component biogenesis organelle organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly centromere complex assembly multi-multicellular organism process female pregnancy embryo implantation multi-organism reproductive process developmental maturation oocyte development anatomical structure maturation oocyte maturation oocyte differentiation cell maturation spermatid development spermatid differentiation negative regulation of cellular component organization regulation of chromosome condensation negative regulation of chromosome condensation negative regulation of chromosome organization negative regulation of organelle organization chromosome condensation subtelomeric heterochromatin formation telomere organization muscle structure development muscle cell differentiation nucleus organization multicellular organism growth developmental growth growth response to organic substance response to stimulus response to hormone response to chemical response to endogenous stimulus	protein-containing complex intracellular anatomical structure chromosome cellular anatomical entity chromosomal region kinetochore intracellular organelle organelle intracellular non-membrane-bounded organelle inner kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome protein-containing complex intracellular anatomical structure chromosome cellular anatomical entity chromosomal region kinetochore intracellular organelle organelle intracellular non-membrane-bounded organelle inner kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome non-membrane-bounded organelle protein-DNA complex nucleosome chromatin membrane-bounded organelle sex chromosome nucleus membrane-enclosed lumen nuclear chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen Barr body nuclear lumen X chromosome nucleoplasm chromosome, telomeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023780	Chromo domain	Domain
A	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A	IPR023779	Chromo domain, conserved site	Conserved Site
A	IPR008251	Chromo shadow domain	Domain
A	IPR000953	Chromo/chromo shadow domain	Domain
A	IPR017984	Chromo domain subgroup	Domain
B	IPR000164	Histone H3/CENP-A	Family
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR007125	Histone H2A/H2B/H3	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
B	M3L	Parent Component: LYS RESID: AA0037 , AA0074 PSI-MOD : O-phospho-L-serine MOD:00046 , N6,N6,N6-trimethyl-L-lysine MOD:00083

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.