3K6G

Crystal structure of Rap1 and TRF2 complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	UBA-like	8054005	3001235	SCOP2B (2022-06-29)
B	SCOP2 Family	Rap1 C-terminal domain	8046769	4005289	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	UBA-like	8054005	3001235	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	UBA-like	8054005	3001235	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rap1-binding motif-like	8092934	3002646	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Rap1-binding motif-like	8092934	3002646	SCOP2B (2022-06-29)
F	SCOP2 Family	Rap1-binding motif-like	8046135	4004895	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Rap1-binding motif-like	8092934	3002646	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)
A	Rap1_C	e3k6gA2	A: alpha arrays	X: Rap1 C-terminal domain (From Topology)	H: Rap1 C-terminal domain (From Topology)	T: Rap1 C-terminal domain	F: Rap1_C	ECOD (1.6)
A	rap1_RCT_1	e3k6gA1	A: alpha arrays	X: Repressor activator protein 1 (RAP1) helical bundle domain (From Topology)	H: Repressor activator protein 1 (RAP1) helical bundle domain (From Topology)	T: Repressor activator protein 1 (RAP1) helical bundle domain	F: rap1_RCT_1	ECOD (1.6)
B	Rap1_C	e3k6gB2	A: alpha arrays	X: Rap1 C-terminal domain (From Topology)	H: Rap1 C-terminal domain (From Topology)	T: Rap1 C-terminal domain	F: Rap1_C	ECOD (1.6)
B	rap1_RCT_1	e3k6gB1	A: alpha arrays	X: Repressor activator protein 1 (RAP1) helical bundle domain (From Topology)	H: Repressor activator protein 1 (RAP1) helical bundle domain (From Topology)	T: Repressor activator protein 1 (RAP1) helical bundle domain	F: rap1_RCT_1	ECOD (1.6)
C	Rap1_C	e3k6gC2	A: alpha arrays	X: Rap1 C-terminal domain (From Topology)	H: Rap1 C-terminal domain (From Topology)	T: Rap1 C-terminal domain	F: Rap1_C	ECOD (1.6)
C	rap1_RCT_1	e3k6gC1	A: alpha arrays	X: Repressor activator protein 1 (RAP1) helical bundle domain (From Topology)	H: Repressor activator protein 1 (RAP1) helical bundle domain (From Topology)	T: Repressor activator protein 1 (RAP1) helical bundle domain	F: rap1_RCT_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF11626	TRF2-interacting telomeric protein/Rap1 - C terminal domain (Rap1_C)	TRF2-interacting telomeric protein/Rap1 - C terminal domain	-	Family
D, E, F	PF16772	Telomeric repeat-binding factor 2 Rap1-binding motif (TERF2_RBM)	Telomeric repeat-binding factor 2 Rap1-binding motif	This domain, found in telomeric repeat-binding factor 2, binds to the C-terminus of repressor activator protein 1 (RAP1) (telomeric repeat-binding factor 2-interacting protein 1) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Telomeric repeat-binding factor 2-interacting protein 1	sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding telomeric DNA binding G-rich strand telomeric DNA binding sequence-specific single stranded DNA binding single-stranded telomeric DNA binding single-stranded DNA binding phosphatase binding protein binding enzyme binding	cellular response to stimulus regulation of DNA recombination regulation of cellular process regulation of double-strand break repair response to stimulus regulation of cellular response to stress regulation of primary metabolic process nucleobase-containing compound metabolic process organic substance metabolic process cellular response to stress response to stress regulation of response to stress recombinational repair regulation of nucleobase-containing compound metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process regulation of double-strand break repair response to stimulus regulation of cellular response to stress regulation of primary metabolic process nucleobase-containing compound metabolic process organic substance metabolic process cellular response to stress response to stress regulation of response to stress recombinational repair regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination DNA repair double-strand break repair regulation of biological process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination organic cyclic compound metabolic process DNA damage response regulation of response to stimulus metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling cellular biosynthetic process telomere organization RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening cellular component organization nucleic acid biosynthetic process organic substance biosynthetic process cellular component organization or biogenesis telomere maintenance via telomerase cellular metabolic process chromosome organization nucleobase-containing compound biosynthetic process macromolecule biosynthetic process telomere maintenance organelle organization biosynthetic process organic cyclic compound biosynthetic process DNA biosynthetic process negative regulation of biological process regulation of DNA recombination at telomere negative regulation of DNA recombination at telomere negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of DNA recombination negative regulation of DNA metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process organonitrogen compound metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of cellular metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation regulation of telomere maintenance regulation of cellular component organization regulation of chromosome organization regulation of organelle organization positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process RNA biosynthetic process positive regulation of molecular function DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process gene expression regulation of cellular biosynthetic process regulation of molecular function regulation of gene expression regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of telomere maintenance negative regulation of chromosome organization negative regulation of cellular component organization negative regulation of organelle organization regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction protein localization localization cellular localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to chromosome, telomeric region positive regulation of organelle organization positive regulation of cellular component organization positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of telomere maintenance positive regulation of nucleobase-containing compound metabolic process positive regulation of chromosome organization positive regulation of DNA metabolic process telomere maintenance in response to DNA damage protection from non-homologous end joining at telomere telomere capping	membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleus nuclear protein-containing complex chromosome cellular anatomical entity intracellular membrane-bounded organelle chromosomal region intracellular organelle organelle telomere cap complex intracellular non-membrane-bounded organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleus nuclear protein-containing complex chromosome cellular anatomical entity intracellular membrane-bounded organelle chromosomal region intracellular organelle organelle telomere cap complex intracellular non-membrane-bounded organelle chromosome, telomeric repeat region chromosome, telomeric region shelterin complex non-membrane-bounded organelle nuclear telomere cap complex cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear chromosome male germ cell nucleus germ cell nucleus nuclear body
D, E, F	Telomeric repeat-binding factor 2	sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding telomeric DNA binding protein-containing complex binding double-stranded telomeric DNA binding double-stranded DNA binding G-rich strand telomeric DNA binding sequence-specific single stranded DNA binding single-stranded telomeric DNA binding single-stranded DNA binding identical protein binding sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding telomeric DNA binding protein-containing complex binding double-stranded telomeric DNA binding double-stranded DNA binding G-rich strand telomeric DNA binding sequence-specific single stranded DNA binding single-stranded telomeric DNA binding single-stranded DNA binding identical protein binding protein binding protein homodimerization activity protein dimerization activity enzyme binding	regulation of catalytic activity biological regulation positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity positive regulation of nitric-oxide synthase activity regulation of molecular function positive regulation of molecular function regulation of monooxygenase activity positive regulation of monooxygenase activity regulation of nitric-oxide synthase activity cellular localization anterograde axonal transport transport regulation of catalytic activity biological regulation positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity positive regulation of nitric-oxide synthase activity regulation of molecular function positive regulation of molecular function regulation of monooxygenase activity positive regulation of monooxygenase activity regulation of nitric-oxide synthase activity cellular localization anterograde axonal transport transport intracellular transport axonal transport establishment of localization localization axo-dendritic transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process microtubule-based movement microtubule-based process regulation of telomere maintenance regulation of cellular component organization regulation of cellular process cellular biosynthetic process telomere organization regulation of DNA biosynthetic process regulation of primary metabolic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening cellular component organization nucleobase-containing compound metabolic process nucleic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process cellular component organization or biogenesis regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of biological process telomere maintenance via telomerase cellular metabolic process chromosome organization primary metabolic process regulation of cellular metabolic process DNA metabolic process regulation of chromosome organization regulation of macromolecule metabolic process regulation of telomere maintenance via telomere lengthening nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of organelle organization regulation of telomere maintenance via telomerase telomere maintenance regulation of cellular biosynthetic process organic cyclic compound metabolic process organelle organization biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process DNA biosynthetic process regulation of DNA metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process gene expression regulation of gene expression positive regulation of gene expression positive regulation of cellular biosynthetic process cellular response to stimulus cellular response to stress response to stimulus response to stress cellular senescence developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development single strand break repair regulation of cellular response to stress negative regulation of biological process negative regulation of DNA repair regulation of response to stress negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process DNA repair negative regulation of macromolecule metabolic process regulation of single strand break repair negative regulation of response to stimulus negative regulation of metabolic process negative regulation of telomere single strand break repair regulation of DNA repair negative regulation of single strand break repair DNA damage response regulation of response to stimulus telomere single strand break repair negative regulation of DNA metabolic process negative regulation of telomere maintenance negative regulation of chromosome organization negative regulation of cellular component organization negative regulation of organelle organization telomeric loop disassembly regulation of telomeric loop disassembly telomeric D-loop disassembly regulation of telomeric D-loop disassembly negative regulation of telomeric D-loop disassembly negative regulation of telomeric loop disassembly protein localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to chromosome, telomeric region positive regulation of organelle organization positive regulation of cellular component organization positive regulation of telomere maintenance positive regulation of nucleobase-containing compound metabolic process positive regulation of chromosome organization positive regulation of DNA metabolic process telomere maintenance in response to DNA damage protection from non-homologous end joining at telomere telomere capping negative regulation of telomere capping regulation of telomere capping protein-containing complex localization axonal transport of messenger ribonucleoprotein complex telomeric loop formation negative regulation of hydrolase activity negative regulation of beta-galactosidase activity regulation of hydrolase activity negative regulation of molecular function negative regulation of catalytic activity regulation of t-circle formation cellular component biogenesis cellular component assembly formation of extrachromosomal circular DNA regulation of cellular component biogenesis negative regulation of t-circle formation telomere maintenance via telomere trimming t-circle formation negative regulation of telomere maintenance via telomerase negative regulation of cellular metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of DNA biosynthetic process negative regulation of telomere maintenance via telomere lengthening negative regulation of biosynthetic process cell cycle regulation of cellular senescence negative regulation of cellular senescence negative regulation of telomere maintenance via semi-conservative replication negative regulation of cell cycle cell cycle DNA replication telomere maintenance via semi-conservative replication regulation of cell cycle process DNA replication nuclear DNA replication regulation of cell cycle cell cycle process DNA-templated DNA replication negative regulation of cell cycle process regulation of telomere maintenance via semi-conservative replication negative regulation of gene expression regulation of nuclease activity negative regulation of exonuclease activity regulation of exonuclease activity negative regulation of nuclease activity regulation of DNA recombination regulation of telomere maintenance via recombination negative regulation of telomere maintenance via recombination negative regulation of DNA recombination at telomere negative regulation of mitotic recombination DNA recombination negative regulation of DNA recombination regulation of DNA recombination at telomere regulation of mitotic recombination telomere maintenance via recombination mitotic recombination	membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleus nuclear protein-containing complex chromosome cellular anatomical entity intracellular membrane-bounded organelle chromosomal region intracellular organelle organelle telomere cap complex intracellular non-membrane-bounded organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleus nuclear protein-containing complex chromosome cellular anatomical entity intracellular membrane-bounded organelle chromosomal region intracellular organelle organelle telomere cap complex intracellular non-membrane-bounded organelle chromosome, telomeric repeat region chromosome, telomeric region shelterin complex non-membrane-bounded organelle nuclear telomere cap complex male germ cell nucleus germ cell nucleus neuron projection cytoplasm axon axon cytoplasm neuron projection cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection cell projection cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR038104	TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily	Homologous Superfamily
A, B, C	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
A, B, C	IPR001357	BRCT domain	Domain
A, B, C	IPR036420	BRCT domain superfamily	Homologous Superfamily
A, B, C	IPR039595	TE2IP/Rap1	Family
A, B, C	IPR021661	TRF2-interacting telomeric protein/Rap1, C-terminal	Domain
A, B, C	IPR015010	Rap1 Myb domain	Domain
D, E, F	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
D, E, F	IPR017357	Telomeric repeat-binding factor 1/2	Family
D, E, F	IPR031902	Telomeric repeat-binding factor 2, Rap1-binding domain	Domain
D, E, F	IPR030657	Telomeric repeat-binding factor 2	Family
D, E, F	IPR017930	Myb domain	Domain
D, E, F	IPR013867	Telomere repeat-binding factor, dimerisation domain	Domain
D, E, F	IPR036507	Telomere repeat-binding factor, dimerisation domain superfamily	Homologous Superfamily
D, E, F	IPR001005	SANT/Myb domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q9NYB0	attention deficit hyperactivity disorder, inattentive type glioblastoma Pick disease dermatomyositis lung carcinoma subependymal giant cell astrocytoma familial melanoma ovarian cancer
D, E, F	Pharos: Q15554	adult T-cell leukemia/lymphoma acute T cell leukemia psoriasis subependymal giant cell astrocytoma osteosarcoma tuberculosis

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.