Annotations: 7V9G

Native BEN4 domain of protein Bend3 with DNA

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	Peptidase_C30	e7v9gJ1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
G	Peptidase_C30	e7v9gG1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
D	Ribosomal_L36	e7v9gD1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L36	ECOD (v294.2)
A	Peptidase_C30	e7v9gA1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J	PF10523	BEN domain (BEN)	BEN domain	The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN do ...	The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription [1]. The BEN domain-containing protein 3 (BEND3) is shown to interact (via BEN domains 1 and 3) with ERCC6L (via N-terminal TPR repeat and SNF2 HeliC region of ERCC6L) which stimulates the ERCC6L translocase and ATPase activities [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L	DNA (5'-D(GPCPAPCPCPGPCPGPTPGPGPGPGPCPCPA)-3')	-	-	-
B, E, H, K	DNA (5'-D(TPGPGPCPCPCPCPAPCPGPCPGPGPTPGPC)-3')	-	-	-
A, D, G, J	BEN domain-containing protein 3	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding rDNA binding	regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization 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 epigenetic regulation of gene expression regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization 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 epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process 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 DNA methylation-dependent constitutive heterochromatin formation cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process ribose phosphate metabolic process ATP metabolic process positive regulation of nucleotide metabolic process positive regulation of biological process carbohydrate derivative metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process regulation of ATP metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process purine nucleotide metabolic process ribonucleotide metabolic process regulation of small molecule metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process phosphorus metabolic process positive regulation of cellular process nucleoside phosphate metabolic process purine nucleoside triphosphate metabolic process positive regulation of phosphorus metabolic process primary metabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process purine-containing compound metabolic process positive regulation of purine nucleotide metabolic process positive regulation of ATP metabolic process organophosphate metabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process positive regulation of small molecule metabolic process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization nucleolar chromatin organization rDNA heterochromatin formation nucleus organization organelle organization nucleolus organization facultative heterochromatin formation	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 chromatin chromosome heterochromatin nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J	IPR033583	BEN domain-containing protein 3	Family
A, D, G, J	IPR018379	BEN domain	Domain

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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.