5WQD | pdb_00005wqd

Crystal structure of TRF2 TRFH in complex with an NBS1 peptide

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G	SCOP2B Superfamily	Telomeric repeat binding factor (TRF) dimerisation domain	8039524	3000229	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Telomeric repeat binding factor (TRF) dimerisation domain	8039524	3000229	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Telomeric repeat binding factor (TRF) dimerisation domain	8039524	3000229	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Telomeric repeat binding factor (TRF) dimerisation domain	8039524	3000229	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Telomeric repeat binding factor (TRF) dimerisation domain	8039524	3000229	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Telomeric repeat binding factor (TRF) dimerisation domain	8039524	3000229	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Telomeric repeat binding factor (TRF) dimerisation domain	8039524	3000229	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)
G	TRF	e5wqdG1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TRF	ECOD (1.6)
F	TRF	e5wqdF1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TRF	ECOD (1.6)
E	TRF	e5wqdE1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TRF	ECOD (1.6)
D	TRF	e5wqdD1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TRF	ECOD (1.6)
C	TRF	e5wqdC1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TRF	ECOD (1.6)
B	TRF	e5wqdB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TRF	ECOD (1.6)
A	TRF	e5wqdA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TRF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	1.25.40.210	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Telomere repeat-binding factor, dimerisation domain	CATH (4.3.0)
F	1.25.40.210	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Telomere repeat-binding factor, dimerisation domain	CATH (4.3.0)
E	1.25.40.210	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Telomere repeat-binding factor, dimerisation domain	CATH (4.3.0)
D	1.25.40.210	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Telomere repeat-binding factor, dimerisation domain	CATH (4.3.0)
C	1.25.40.210	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Telomere repeat-binding factor, dimerisation domain	CATH (4.3.0)
B	1.25.40.210	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Telomere repeat-binding factor, dimerisation domain	CATH (4.3.0)
A	1.25.40.210	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Telomere repeat-binding factor, dimerisation domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G	PF08558	Telomere repeat binding factor (TRF) (TRF)	Telomere repeat binding factor (TRF)	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G	Telomeric repeat-binding factor 2	sequence-specific DNA binding DNA binding binding nucleic acid binding telomeric DNA 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 sequence-specific DNA binding DNA binding binding nucleic acid binding telomeric DNA 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 protein-containing complex binding enzyme binding	cellular localization transport intracellular transport axonal transport establishment of localization localization axo-dendritic transport axonal transport of messenger ribonucleoprotein complex establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process microtubule-based movement cellular localization transport intracellular transport axonal transport establishment of localization localization axo-dendritic transport axonal transport of messenger ribonucleoprotein complex establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process microtubule-based movement microtubule-based process telomere organization chromosome organization primary metabolic process DNA metabolic process telomeric loop formation nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organelle organization metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of telomere maintenance regulation of cellular component organization regulation of cellular process regulation of DNA biosynthetic process regulation of primary metabolic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening nucleic acid biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of biological process telomere maintenance via telomerase biological regulation regulation of chromosome organization regulation of macromolecule metabolic process regulation of telomere maintenance via telomere lengthening nucleobase-containing compound biosynthetic process macromolecule biosynthetic process regulation of organelle organization regulation of telomere maintenance via telomerase biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process DNA biosynthetic process regulation of DNA metabolic process regulation of t-circle formation negative regulation of biological process cellular component biogenesis cellular component assembly negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of cellular component organization formation of extrachromosomal circular DNA negative regulation of metabolic process regulation of cellular component biogenesis negative regulation of t-circle formation telomere maintenance via telomere trimming t-circle formation negative regulation of DNA metabolic process cellular response to stimulus cellular response to stress response to stimulus response to stress cellular senescence telomeric loop disassembly telomeric D-loop disassembly 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 negative regulation of telomere maintenance negative regulation of telomere maintenance via telomerase negative regulation of chromosome organization negative regulation of macromolecule biosynthetic process negative regulation of DNA biosynthetic process negative regulation of telomere maintenance via telomere lengthening negative regulation of organelle organization negative regulation of biosynthetic process single strand break repair regulation of cellular response to stress negative regulation of DNA repair regulation of response to stress DNA repair regulation of single strand break repair negative regulation of response to stimulus 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 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 cell cycle 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 regulation of telomeric loop disassembly regulation of telomeric D-loop disassembly negative regulation of telomeric D-loop disassembly negative regulation of telomeric loop disassembly protein localization to chromosome protein localization to organelle macromolecule localization protein localization to chromosome, telomeric region intracellular protein localization positive regulation of organelle organization positive regulation of cellular component organization positive regulation of biological process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of telomere maintenance 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 regulation of DNA recombination regulation of telomere maintenance via recombination regulation of DNA recombination at telomere regulation of mitotic recombination negative regulation of telomere maintenance via recombination telomere maintenance via recombination negative regulation of DNA recombination at telomere negative regulation of mitotic recombination DNA recombination mitotic recombination negative regulation of DNA recombination	membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleus intracellular membraneless organelle nuclear protein-containing complex chromosome intracellular membrane-bounded organelle chromosomal region intracellular organelle cellular anatomical structure organelle telomere cap complex membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleus intracellular membraneless organelle nuclear protein-containing complex chromosome intracellular membrane-bounded organelle chromosomal region intracellular organelle cellular anatomical structure organelle telomere cap complex membraneless organelle chromosome, telomeric repeat region chromosome, telomeric region shelterin complex nuclear telomere cap complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen axon cell projection neuron projection plasma membrane bounded cell projection male germ cell nucleus germ cell nucleus nuclear body
H, I, J, K, L H, I, J, K, L, M, N	Nibrin	protein binding binding histone binding chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity protein binding binding histone binding chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity DNA binding damaged DNA binding nucleic acid binding transcription factor binding DNA-binding transcription factor binding phosphorylation-dependent protein binding modification-dependent protein binding	developmental process neuroblast proliferation multicellular organismal process cell population proliferation cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development cell differentiation anatomical structure development cellular process neural precursor cell proliferation system development developmental process neuroblast proliferation multicellular organismal process cell population proliferation cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development cell differentiation anatomical structure development cellular process neural precursor cell proliferation system development cellular response to stimulus telomere maintenance in response to DNA damage response to stimulus telomere organization chromosome organization primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organelle organization cellular response to stress DNA damage response response to stress metabolic process cellular component organization or biogenesis macromolecule metabolic process double-strand break repair DNA double-strand break processing DNA repair localization protein localization to chromosome protein localization to organelle macromolecule localization protein localization to site of double-strand break intracellular protein localization homologous recombination DNA recombination developmental growth chordate embryonic development growth embryo development in utero embryonic development embryo development ending in birth or egg hatching blastocyst growth blastocyst development formation of extrachromosomal circular DNA cellular component biogenesis cellular component assembly telomere maintenance via telomere trimming t-circle formation regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress recombinational repair positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination positive regulation of cellular process positive regulation of DNA recombination regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of double-strand break repair regulation of DNA repair regulation of double-strand break repair via homologous recombination positive regulation of DNA metabolic process regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process positive regulation of organelle organization regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization positive regulation of telomere maintenance regulation of chromosome organization regulation of organelle organization positive regulation of chromosome organization protection from non-homologous end joining at telomere telomere capping immune system development adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity immunoglobulin production immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination B cell activation involved in immune response lymphocyte activation cell activation involved in immune response leukocyte activation somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response leukocyte mediated immunity somatic diversification of immune receptors lymphocyte activation involved in immune response somatic recombination of immunoglobulin genes involved in immune response production of molecular mediator of immune response immune response B cell activation cell activation gene expression macromolecule biosynthetic process immunoglobulin mediated immune response adaptive immune response immune effector process somatic diversification of immunoglobulins biosynthetic process immune system process somatic diversification of immune receptors via germline recombination within a single locus B cell mediated immunity isotype switching double-strand break repair via nonhomologous end joining double-strand break repair via alternative nonhomologous end joining regulation of cell cycle phase transition signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint cell communication regulation of mitotic cell cycle negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition negative regulation of telomere maintenance negative regulation of chromosome organization negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of cellular component organization negative regulation of metabolic process negative regulation of organelle organization negative regulation of telomere capping negative regulation of DNA metabolic process regulation of telomere capping DNA damage checkpoint signaling DNA integrity checkpoint signaling signal transduction in response to DNA damage cell death apoptotic signaling pathway apoptotic process intrinsic apoptotic signaling pathway programmed cell death chromatin organization chromatin remodeling R-loop processing system process nervous system process neuromuscular process neuromuscular process controlling balance telomeric 3' overhang formation DNA strand elongation regulation of DNA-templated DNA replication initiation DNA-templated DNA replication DNA replication initiation DNA replication regulation of DNA-templated DNA replication regulation of DNA replication DNA-templated DNA replication maintenance of fidelity DNA strand resection involved in replication fork processing replication fork processing mitotic G2 DNA damage checkpoint signaling mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling protein polyubiquitination protein K63-linked ubiquitination protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal signal transduction by p53 class mediator DNA damage response, signal transduction by p53 class mediator sexual reproduction reproductive process meiotic cell cycle	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure BRCA1-C complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cytoplasm cytosol Golgi apparatus endomembrane system membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure BRCA1-C complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cytoplasm cytosol Golgi apparatus endomembrane system inclusion body nuclear inclusion body membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen nucleoplasm replication fork Mre11 complex site of double-strand break site of DNA damage nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR031902	Telomeric repeat-binding factor 2, Rap1-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR030657	Telomeric repeat-binding factor 2	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR017930	Myb domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR013867	Telomere repeat-binding factor, dimerisation domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR036507	Telomere repeat-binding factor, dimerisation domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR017357	Telomeric repeat-binding factor 1/2	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR001005	SANT/Myb domain	Domain
H, I, J, K, L H, I, J, K, L, M, N	IPR032429	Nibrin, second BRCT domain	Domain
H, I, J, K, L H, I, J, K, L, M, N	IPR040227	Nibrin-related	Family
H, I, J, K, L H, I, J, K, L, M, N	IPR013908	Nibrin, C-terminal	Domain
H, I, J, K, L H, I, J, K, L, M, N	IPR043014	Nibrin, second BRCT domain superfamily	Homologous Superfamily
H, I, J, K, L H, I, J, K, L, M, N	IPR001357	BRCT domain	Domain
H, I, J, K, L H, I, J, K, L, M, N	IPR036420	BRCT domain superfamily	Homologous Superfamily
H, I, J, K, L H, I, J, K, L, M, N	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
H, I, J, K, L H, I, J, K, L, M, N	IPR000253	Forkhead-associated (FHA) domain	Domain
H, I, J, K, L H, I, J, K, L, M, N	IPR016592	Nibrin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G	Pharos: Q15554	adult T-cell leukemia/lymphoma acute T cell leukemia psoriasis subependymal giant cell astrocytoma osteosarcoma tuberculosis
H, I, J, K, L H, I, J, K, L, M, N	Pharos: O60934	Nijmegen breakage syndrome prostate cancer aplastic anemia ovarian cancer breast cancer Neoplasm Recurrence, Local stomatitis lung cancer medulloblastoma cancer Crohn disease rhabdomyosarcoma familial prostate carcinoma ulcerative colitis hematopoietic and lymphoid system neoplasm Nijmegen breakage syndrome prostate cancer aplastic anemia ovarian cancer breast cancer Neoplasm Recurrence, Local stomatitis lung cancer medulloblastoma cancer Crohn disease rhabdomyosarcoma familial prostate carcinoma ulcerative colitis hematopoietic and lymphoid system neoplasm leukemia, acute lymphocytic, susceptibility to, 1 lymphoplasmacytic lymphoma microcephaly non-Hodgkin lymphoma pituitary cancer childhood acute lymphoblastic leukemia Sjogren syndrome gastric carcinoma hereditary breast carcinoma idiopathic aplastic anemia osteogenesis imperfecta plasma cell myeloma congenital anemia psoriasis Emery-Dreifuss muscular dystrophy glioma hereditary breast ovarian cancer syndrome intellectual disability

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.