2RVN | pdb_00002rvn

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity 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 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 regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process cellular developmental process ossification cell differentiation 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 negative regulation of biological process cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule 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 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 protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization protein-containing complex assembly nucleosome assembly nucleosome organization spermatid development spermatid differentiation negative regulation of cellular component organization regulation of chromosome condensation chromosome organization regulation of chromosome organization regulation of organelle organization negative regulation of chromosome condensation organelle organization negative regulation of chromosome organization negative regulation of organelle organization chromosome condensation subtelomeric heterochromatin formation muscle structure development muscle cell differentiation nucleus organization multicellular organism growth developmental growth	protein-containing complex intracellular anatomical structure intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle cellular anatomical structure organelle membraneless organelle inner kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex protein-containing complex intracellular anatomical structure intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle cellular anatomical structure organelle membraneless organelle inner kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome 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
A	Chromobox protein homolog 5	histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone deacetylase binding protein binding binding enzyme binding chromatin binding ribonucleoprotein complex binding protein-containing complex binding transcription factor binding histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone deacetylase binding protein binding binding enzyme binding chromatin binding ribonucleoprotein complex binding protein-containing complex binding transcription factor binding DNA-binding transcription factor 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 RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription 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 RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule 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 transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex histone methyltransferase complex catalytic complex nuclear protein-containing complex transferase complex nucleoplasm methyltransferase complex pericentric heterochromatin 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B	IPR000164	Histone H3/CENP-A	Family
B	IPR009072	Histone-fold	Homologous Superfamily
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	IPR051219	Heterochromatin-associated chromo domain-containing protein	Family
A	IPR000953	Chromo/chromo shadow domain	Domain
A	IPR017984	Chromo domain subgroup	Domain

Protein Modification Annotation

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.