7VYW | pdb_00007vyw

Crystal structure of the chromodomain of Arabidopsis LHP1 in complex with methylated histone H3K9 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	8106633	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	Ribosomal_L19	e7vywA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.1)

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	methylated histone H3K9 peptide	-	-	-
A	Chromo domain-containing protein LHP1	chromatin binding binding RNA binding nucleic acid binding sequence-specific DNA binding DNA binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines GTP cyclohydrolase II activity GTP cyclohydrolase activity cyclohydrolase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding chromatin binding binding RNA binding nucleic acid binding sequence-specific DNA binding DNA binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines GTP cyclohydrolase II activity GTP cyclohydrolase activity cyclohydrolase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding	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 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 cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process cellular developmental process cell differentiation response to stimulus vernalization response response to stress response to abiotic stimulus response to cold response to temperature stimulus response to light stimulus photoperiodism response to radiation growth cell growth multidimensional cell growth response to carbohydrate response to sucrose response to disaccharide response to chemical response to oxygen-containing compound cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic photoperiodism, flowering multicellular organismal process reproductive system development reproductive process vegetative to reproductive phase transition of meristem developmental process involved in reproduction multicellular organism development anatomical structure development reproductive structure development post-embryonic development system development anatomical structure morphogenesis shoot system development shoot system morphogenesis flower development reproductive shoot system development cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization regulation of developmental process regulation of reproductive process negative regulation of post-embryonic development negative regulation of flower development regulation of multicellular organismal process regulation of flower development regulation of multicellular organismal development negative regulation of developmental process regulation of shoot system development regulation of post-embryonic development negative regulation of reproductive process negative regulation of multicellular organismal process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin euchromatin membrane-bounded organelle plastid cytoplasm intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin euchromatin membrane-bounded organelle plastid cytoplasm intracellular membrane-bounded organelle chloroplast nucleus

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	IPR044251	Chromo domain-containing protein LHP1	Family
A	IPR008251	Chromo shadow domain	Domain
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
B	PCA	Parent Component: GLN RESID: AA0074 , AA0031 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083 , 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.