4BJ5

Crystal structure of Rif2 in complex with the C-terminal domain of Rap1 (Rap1-RCT)

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	UBA-like	8054004	3001235	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	UBA-like	8054004	3001235	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)
A	PF21450	e4bj5A2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF21450	ECOD (1.6)
A	PF21449	e4bj5A3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF21449	ECOD (1.6)
B	PF21450	e4bj5B2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF21450	ECOD (1.6)
B	PF21449	e4bj5B3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF21449	ECOD (1.6)
C	PF11626	e4bj5C3	A: alpha arrays	X: Rap1 C-terminal domain (From Topology)	H: Rap1 C-terminal domain (From Topology)	T: Rap1 C-terminal domain	F: PF11626	ECOD (1.6)
C	PF11626	e4bj5C4	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: PF11626	ECOD (1.6)
E	PF11626	e4bj5E3	A: alpha arrays	X: Rap1 C-terminal domain (From Topology)	H: Rap1 C-terminal domain (From Topology)	T: Rap1 C-terminal domain	F: PF11626	ECOD (1.6)
E	PF11626	e4bj5E4	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: PF11626	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.1650	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
A	3.40.50.12060	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	1.20.120.1650	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
B	3.40.50.12060	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	1.20.120.1480	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
C	1.10.10.2170	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
E	1.20.120.1480	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
E	1.10.10.2170	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21450	RIF2, AAA+ lid domain (RIF2_lid)	RIF2, AAA+ lid domain	RIF2 is involved in transcriptional silencing and telomere length regulation [1]. It belongs to the ATPase family associated with diverse cellular activities. This domain represents the alpha-helical AAA+ lid domain described in [1].	Domain
C, E	PF11626	TRF2-interacting telomeric protein/Rap1 - C terminal domain (Rap1_C)	TRF2-interacting telomeric protein/Rap1 - C terminal domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PROTEIN RIF2	sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding telomeric DNA binding	telomere organization chromosome organization primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organic cyclic compound metabolic process organelle organization organic substance metabolic process telomere capping cellular process metabolic process telomere organization chromosome organization primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organic cyclic compound metabolic process organelle organization organic substance metabolic process telomere capping cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process cellular biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening nucleic acid biosynthetic process organic substance biosynthetic process telomere maintenance via telomerase cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process biosynthetic process organic cyclic compound biosynthetic process DNA biosynthetic process	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region cellular anatomical entity chromosomal region non-membrane-bounded organelle membrane-bounded organelle protein-containing complex protein-DNA complex nucleus nuclear protein-containing complex intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region cellular anatomical entity chromosomal region non-membrane-bounded organelle membrane-bounded organelle protein-containing complex protein-DNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle telomere cap complex chromosome, telomeric repeat region shelterin complex nuclear telomere cap complex
C, E	DNA-BINDING PROTEIN RAP1	TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding histone binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding transcription regulator activity DNA-binding transcription factor activity TFIID-class transcription factor complex binding transcription factor binding basal transcription machinery binding protein-containing complex binding protein binding binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding histone binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding DNA binding organic cyclic compound binding nucleic acid binding telomeric DNA binding G-quadruplex DNA binding double-stranded telomeric DNA binding double-stranded DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific sequence-specific double-stranded DNA binding transcription cis-regulatory region binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding TBP-class protein binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding DNA binding, bending	regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process 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 protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular 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 silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process oxoacid metabolic process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process organic acid metabolic process regulation of primary metabolic process regulation of ATP metabolic process nucleobase-containing compound metabolic process regulation of purine nucleotide catabolic process regulation of small molecule metabolic process glycolytic process regulation of nucleotide metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process organonitrogen compound catabolic process nicotinamide nucleotide metabolic process regulation of carbohydrate catabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of nucleotide catabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process catabolic process ATP metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process regulation of carbohydrate metabolic process nucleotide catabolic process ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process carbohydrate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process ADP catabolic process carboxylic acid metabolic process regulation of catabolic process generation of precursor metabolites and energy regulation of glycolytic process organic cyclic compound catabolic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process organic substance catabolic process purine ribonucleoside diphosphate catabolic process telomere organization chromosome organization DNA metabolic process nucleic acid metabolic process telomere maintenance organelle organization establishment of protein localization to telomere protein localization establishment of protein localization cellular localization protein localization to chromosome, telomeric region establishment of localization localization establishment of protein localization to organelle protein localization to chromosome cellular macromolecule localization macromolecule localization protein localization to organelle establishment of protein localization to chromosome G-quadruplex DNA formation regulation of ribosomal protein gene transcription by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process organic cyclic compound biosynthetic process positive regulation of ribosomal protein gene transcription by RNA polymerase II regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process subtelomeric heterochromatin formation cellular response to stimulus telomere maintenance in response to DNA damage response to stimulus cellular response to stress response to stress protection from non-homologous end joining at telomere telomere capping DNA damage response negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process telomere maintenance via telomere lengthening protein localization to chromatin establishment of protein localization to chromatin	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 cytosol transcription regulator complex membrane-enclosed lumen nuclear chromosome intracellular organelle lumen organelle lumen nuclear lumen
D, F	DNA-BINDING PROTEIN RAP1	sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding telomeric DNA binding	telomere organization chromosome organization primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organic cyclic compound metabolic process organelle organization organic substance metabolic process telomere capping cellular process metabolic process telomere organization chromosome organization primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organic cyclic compound metabolic process organelle organization organic substance metabolic process telomere capping cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process cellular biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening nucleic acid biosynthetic process organic substance biosynthetic process telomere maintenance via telomerase cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process biosynthetic process organic cyclic compound biosynthetic process DNA biosynthetic process	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region cellular anatomical entity chromosomal region non-membrane-bounded organelle membrane-bounded organelle protein-containing complex protein-DNA complex nucleus nuclear protein-containing complex intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region cellular anatomical entity chromosomal region non-membrane-bounded organelle membrane-bounded organelle protein-containing complex protein-DNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle telomere cap complex chromosome, telomeric repeat region shelterin complex nuclear telomere cap complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR049045	RIF2, AAA+ lid domain	Domain
A, B	IPR049044	RIF2, ASCE domain	Domain
C, E	IPR038104	TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily	Homologous Superfamily
C, E	IPR017930	Myb domain	Domain
C, E	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
C, E	IPR001357	BRCT domain	Domain
C, E	IPR015280	Rap1, DNA-binding domain	Domain
C, E	IPR036420	BRCT domain superfamily	Homologous Superfamily
C, E	IPR039595	TE2IP/Rap1	Family
C, E	IPR021661	TRF2-interacting telomeric protein/Rap1, C-terminal	Domain
C, E	IPR001005	SANT/Myb domain	Domain
D, F	IPR049045	RIF2, AAA+ lid domain	Domain
D, F	IPR049044	RIF2, ASCE domain	Domain

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 R01GM133198.