1CF7

STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d1cf7a_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Cell cycle transcription factor e2f-dp	Cell cycle transcription factor E2F-4	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d1cf7b_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Cell cycle transcription factor e2f-dp	Cell cycle transcription factor DP-2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2 Family	E2F/DP DNA-binding domain-like	8003053	4000205	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Winged helix DNA-binding domain	8003054	3000034	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Family	E2F/DP DNA-binding domain-like	8003056	4000205	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Superfamily	Winged helix DNA-binding domain	8057678	3000034	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth A]	PF02319	e1cf7A1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF02319	ECOD (1.6)
D [auth B]	PF02319	e1cf7B1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF02319	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D [auth B]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF02319	E2F/DP family winged-helix DNA-binding domain (E2F_TDP)	E2F/DP family winged-helix DNA-binding domain	This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having incre ...	This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins.	Domain
D [auth B]	PF02319	E2F/DP family winged-helix DNA-binding domain (E2F_TDP)	E2F/DP family winged-helix DNA-binding domain	This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having incre ...	This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	DNA (5'-D(APTPTPTPTPCPGPCPGPCPGPGPTPTPTPT)-3')	-	-	-
B [auth D]	DNA (5'-D(TPAPAPAPAPCPCPGPCPGPCPGPAPAPAPA)-3')	-	-	-
C [auth A]	PROTEIN (TRANSCRIPTION FACTOR E2F-4)	protein binding binding protein domain specific binding DNA binding sequence-specific DNA 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 binding binding protein domain specific binding DNA binding sequence-specific DNA 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 transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity protein-containing complex binding chromatin binding promoter-specific chromatin binding DNA-binding transcription factor activity, RNA polymerase II-specific protein dimerization activity DNA-binding transcription activator activity, RNA polymerase II-specific	organelle assembly plasma membrane bounded cell projection organization motile cilium assembly cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization organelle organization cellular component assembly cilium assembly cellular process cellular component organization or biogenesis cilium organization cell projection assembly organelle assembly plasma membrane bounded cell projection organization motile cilium assembly cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization organelle organization cellular component assembly cilium assembly cellular process cellular component organization or biogenesis cilium organization cell projection assembly developmental process anatomical structure morphogenesis animal organ development anatomical structure development animal organ morphogenesis regulation of cellular component size homeostatic process cell volume homeostasis biological regulation cellular homeostasis regulation of biological quality regulation of cell size regulation of anatomical structure size epithelium development cellular developmental process cell differentiation tissue development epithelial cell differentiation multi-ciliated epithelial cell differentiation cell cycle centriole assembly microtubule organizing center organization non-membrane-bounded organelle assembly microtubule cytoskeleton organization microtubule-based process cytoskeleton organization regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression 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 positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process epithelial cell development cell development multicellular organismal process system process circulatory system process blood circulation	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle
D [auth B]	PROTEIN (TRANSCRIPTION FACTOR DP-2)	DNA binding binding organic cyclic compound binding nucleic acid binding transcription factor binding protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein domain specific binding	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 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 cellular process cell cycle developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development transcription by RNA polymerase II regulation of transcription by RNA polymerase II regulation of cell cycle positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle mitotic spindle cytoskeleton spindle RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle mitotic spindle cytoskeleton spindle intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-DNA complex chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR032198	E2F transcription factor, CC-MB domain	Domain
C [auth A]	IPR037241	E2F-DP heterodimerization region	Homologous Superfamily
C [auth A]	IPR003316	E2F/DP family, winged-helix DNA-binding domain	Domain
C [auth A]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C [auth A]	IPR015633	E2F Family	Family
C [auth A]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
D [auth B]	IPR014889	Transcription factor DP, C-terminal	Domain
D [auth B]	IPR037241	E2F-DP heterodimerization region	Homologous Superfamily
D [auth B]	IPR003316	E2F/DP family, winged-helix DNA-binding domain	Domain
D [auth B]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
D [auth B]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
D [auth B]	IPR015648	Transcription factor DP	Family
D [auth B]	IPR038168	Transcription factor DP, C-terminal domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A]	Pharos: Q16254	cancer ovarian cancer malignant mesothelioma retinal disease osteosarcoma
D [auth B]	Pharos: Q14188	malignant mesothelioma atopic eczema glioblastoma osteosarcoma primitive neuroectodermal tumor testicular germ cell tumor atypical teratoid rhabdoid tumor invasive ductal breast carcinoma medulloblastoma ovarian cancer psoriasis cystic fibrosis lung cancer non-small cell lung carcinoma Pick disease malignant mesothelioma atopic eczema glioblastoma osteosarcoma primitive neuroectodermal tumor testicular germ cell tumor atypical teratoid rhabdoid tumor invasive ductal breast carcinoma medulloblastoma ovarian cancer psoriasis cystic fibrosis lung cancer non-small cell lung carcinoma Pick disease sinusitis

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.