4M7C | pdb_00004m7c

Crystal structure of the TRF2-binding motif of SLX4 in complex with the TRFH domain of TRF2

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)
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)
B	TRF	e4m7cB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TRF	ECOD (1.6)
A	TRF	e4m7cA1	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)
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	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
C, D	Peptide from Structure-specific endonuclease subunit SLX4	DNA binding binding nucleic acid binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	positive regulation of organelle organization regulation of telomere maintenance regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization regulation of t-circle formation positive regulation of biological process telomere organization regulation of primary metabolic process cellular component biogenesis cellular component organization nucleobase-containing compound metabolic process positive regulation of metabolic process cellular component assembly positive regulation of organelle organization regulation of telomere maintenance regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization regulation of t-circle formation positive regulation of biological process telomere organization regulation of primary metabolic process cellular component biogenesis cellular component organization nucleobase-containing compound metabolic process positive regulation of metabolic process cellular component assembly positive regulation of macromolecule metabolic process cellular component organization or biogenesis regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process positive regulation of telomere maintenance formation of extrachromosomal circular DNA positive regulation of cellular component biogenesis biological regulation chromosome organization primary metabolic process DNA metabolic process regulation of chromosome organization regulation of macromolecule metabolic process regulation of cellular component biogenesis nucleic acid metabolic process regulation of organelle organization positive regulation of chromosome organization telomere maintenance organelle organization positive regulation of DNA metabolic process telomere maintenance via telomere trimming t-circle formation cellular process metabolic process positive regulation of t-circle formation macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA replication cellular response to stimulus double-strand break repair response to stimulus DNA recombination cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process meiosis I meiotic nuclear division cell cycle reciprocal homologous recombination cell cycle process meiotic cell cycle organelle fission reciprocal meiotic recombination nuclear division meiosis I cell cycle process negative regulation of telomere maintenance negative regulation of telomere maintenance via telomere lengthening negative regulation of biological process telomere maintenance via telomere lengthening negative regulation of chromosome organization 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 negative regulation of metabolic process regulation of telomere maintenance via telomere lengthening negative regulation of organelle organization negative regulation of DNA metabolic process nucleotide-excision repair DNA double-strand break processing double-strand break repair via single-strand annealing DNA double-strand break processing involved in repair via single-strand annealing response to endogenous stimulus response to intra-S DNA damage checkpoint signaling response to biotic stimulus cellular response to biotic stimulus cellular response to endogenous stimulus response to DNA integrity checkpoint signaling response to DNA damage checkpoint signaling response to cell cycle checkpoint signaling telomeric loop disassembly telomeric D-loop disassembly	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle Slx1-Slx4 complex nuclear lumen chromosome, telomeric region chromosomal region nucleoplasm chromatin
A, B	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR018574	Structure-specific endonuclease subunit Slx4	Family
C, D	IPR000210	BTB/POZ domain	Domain
C, D	IPR006642	Rad18, zinc finger UBZ4-type	Domain
C, D	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
A, B	IPR031902	Telomeric repeat-binding factor 2, Rap1-binding domain	Domain
A, B	IPR030657	Telomeric repeat-binding factor 2	Family
A, B	IPR017930	Myb domain	Domain
A, B	IPR013867	Telomere repeat-binding factor, dimerisation domain	Domain
A, B	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B	IPR036507	Telomere repeat-binding factor, dimerisation domain superfamily	Homologous Superfamily
A, B	IPR017357	Telomeric repeat-binding factor 1/2	Family
A, B	IPR001005	SANT/Myb domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q8IY92	Fanconi anemia Fanconi anemia complementation group P aplastic anemia Esophageal atresia with or without tracheoesophageal fistula hereditary breast carcinoma congenital anemia esophageal atresia/tracheoesophageal fistula inherited aplastic anemia neurofibromatosis type 1 hematopoietic and lymphoid system neoplasm intellectual disability osteosarcoma
A, B	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 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.