5Z8N | pdb_00005z8n

Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth C]	PHD,BAH_1	e5z8nC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PHD,BAH_1	ECOD (1.6)
C [auth B]	PHD,BAH_1	e5z8nB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PHD,BAH_1	ECOD (1.6)
A	PHD,BAH_1	e5z8nA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PHD,BAH_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth C]	2.30.30.490	Mainly Beta	Roll	SH3 type barrels.	Bromo adjacent homology (BAH) domain	CATH (utative)
E [auth C]	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
C [auth B]	2.30.30.490	Mainly Beta	Roll	SH3 type barrels.	Bromo adjacent homology (BAH) domain	CATH (utative)
A	2.30.30.490	Mainly Beta	Roll	SH3 type barrels.	Bromo adjacent homology (BAH) domain	CATH (utative)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth C]	PF01426	BAH domain (BAH)	BAH domain	This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction [3].	Domain
A, C [auth B], E [auth C]	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth P], D [auth Q], F [auth R]	H3K4me2 peptide	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle extracellular region membraneless organelle intracellular membraneless organelle chromocenter cytosol cell periphery membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle extracellular region membraneless organelle intracellular membraneless organelle chromocenter cytosol cell periphery plasma membrane membrane protein-containing complex protein-DNA complex nucleosome chromatin chromosome nucleus
A, C [auth B], E [auth C]	Chromatin remodeling protein EBS	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding molecular function inhibitor activity molecular function regulator activity chromatin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	photoperiodism, flowering developmental process response to light stimulus multicellular organismal process regulation of biological process reproductive system development response to stimulus reproductive process biological regulation vegetative to reproductive phase transition of meristem developmental process involved in reproduction multicellular organism development photoperiodism regulation of response to stimulus anatomical structure development photoperiodism, flowering developmental process response to light stimulus multicellular organismal process regulation of biological process reproductive system development response to stimulus reproductive process biological regulation vegetative to reproductive phase transition of meristem developmental process involved in reproduction multicellular organism development photoperiodism regulation of response to stimulus anatomical structure development reproductive structure development post-embryonic development response to radiation response to abiotic stimulus regulation of photoperiodism, flowering system development flower development reproductive shoot system development shoot system development regulation of developmental process negative regulation of biological process regulation of long-day photoperiodism, flowering negative regulation of long-day photoperiodism, flowering negative regulation of post-embryonic development regulation of multicellular organismal process long-day photoperiodism regulation of multicellular organismal development negative regulation of response to stimulus negative regulation of developmental process regulation of post-embryonic development long-day photoperiodism, flowering negative regulation of multicellular organismal process seed germination seedling development regulation of cellular process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process epigenetic regulation of gene expression negative regulation of metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression 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 cellular process macromolecule metabolic process regulation of metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth P], D [auth Q], F [auth R]	IPR009072	Histone-fold	Homologous Superfamily
B [auth P], D [auth Q], F [auth R]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B [auth P], D [auth Q], F [auth R]	IPR000164	Histone H3/CENP-A	Family
A, C [auth B], E [auth C]	IPR001965	Zinc finger, PHD-type	Domain
A, C [auth B], E [auth C]	IPR043151	Bromo adjacent homology (BAH) domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C [auth B], E [auth C]	IPR001025	Bromo adjacent homology (BAH) domain	Domain
A, C [auth B], E [auth C]	IPR019787	Zinc finger, PHD-finger	Domain
A, C [auth B], E [auth C]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, C [auth B], E [auth C]	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth P], D [auth Q], F [auth R]	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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.