4BJ5 | pdb_00004bj5

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)
E	SCOP2B Superfamily	UBA-like	8054004	3001235	SCOP2B (2022-06-29)
C	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	Choline_kinase, EcKL	e4bj5A2	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Choline_kinase, EcKL	ECOD (v294.1)
A	Ldl_recept_a	e4bj5A3	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Ldl_recept_a	ECOD (v294.1)
B	Choline_kinase, EcKL	e4bj5B2	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Choline_kinase, EcKL	ECOD (v294.1)
B	Ldl_recept_a	e4bj5B3	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Ldl_recept_a	ECOD (v294.1)
E	SRP_SPB	e4bj5E3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: SRP_SPB	ECOD (v294.1)
C	SRP_SPB	e4bj5C3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: SRP_SPB	ECOD (v294.1)

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)
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)
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)

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 nucleic acid binding telomeric repeat 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 organelle organization telomere capping cellular process metabolic process cellular component organization or biogenesis macromolecule 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 organelle organization telomere capping cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process telomere maintenance via telomerase nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-bounded organelle protein-containing complex protein-DNA complex nucleus nuclear protein-containing complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region 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 RNA polymerase binding protein binding binding RNA polymerase II complex binding general transcription initiation factor binding RNA polymerase core enzyme binding enzyme 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 TFIID-class transcription factor complex binding transcription factor binding RNA polymerase binding protein binding binding RNA polymerase II complex binding general transcription initiation factor binding RNA polymerase core enzyme binding enzyme 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 telomeric G-quadruplex DNA binding DNA binding sequence-specific DNA binding G-quadruplex DNA binding nucleic acid binding telomeric repeat 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 protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding DNA binding, bending	regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization 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 epigenetic regulation of gene expression regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization 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 epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule 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 cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration 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 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 nucleoside phosphate metabolic 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 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 cellular respiration catabolic process ATP metabolic process energy derivation by oxidation of organic compounds 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 purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process regulation of catabolic process generation of precursor metabolites and energy regulation of glycolytic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic 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 localization establishment of protein localization establishment of protein localization to organelle establishment of protein localization to chromosome establishment of localization G-quadruplex DNA formation regulation of ribosomal protein gene transcription by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of ribosomal protein gene transcription by RNA polymerase II regulation of DNA-templated transcription subtelomeric heterochromatin formation cellular response to stimulus telomere maintenance in response to DNA damage response to stimulus protection from non-homologous end joining at telomere cellular response to stress telomere capping DNA damage response response to stress 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 establishment of protein localization to chromatin	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 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 nucleic acid binding telomeric repeat 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 organelle organization telomere capping cellular process metabolic process cellular component organization or biogenesis macromolecule 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 organelle organization telomere capping cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process telomere maintenance via telomerase nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-bounded organelle protein-containing complex protein-DNA complex nucleus nuclear protein-containing complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region 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	IPR001357	BRCT domain	Domain
C, E	IPR015280	Rap1, DNA-binding domain	Domain
C, E	IPR036420	BRCT domain superfamily	Homologous Superfamily
C, E	IPR009057	Homedomain-like 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.