4FBW

Crystal structure of an unfused Mre11-Nbs1 complex with two manganese ions per active site

External Resource: Annotation

Domain Annotation: SCOP2 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)
A	SCOP2B Superfamily	Metallo-dependent phosphatases	8090752	3001067	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mre11 C-terminal domain-like	8090753	3002453	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Mre11 C-terminal domain-like	8090753	3002453	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent phosphatases	8090752	3001067	SCOP2B (2022-06-29)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
A	3.30.110.110	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	Mre11, capping domain	CATH (4.3.0)
B	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
B	3.30.110.110	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	Mre11, capping domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00149	Calcineurin-like phosphoesterase (Metallophos)	Calcineurin-like phosphoesterase	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or ...	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829. The most conserved regions in this superfamily centre around the metal chelating residues.	Domain
A, B	PF04152	Mre11 DNA-binding presumed domain (Mre11_DNA_bind)	Mre11 DNA-binding presumed domain	The Mre11 complex is a multi-subunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication [1]. Mre11 has an intrinsic DNA-binding activity that is stimulated by Rad50 on its own or in ...	The Mre11 complex is a multi-subunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication [1]. Mre11 has an intrinsic DNA-binding activity that is stimulated by Rad50 on its own or in combination with Nbs1 [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA repair protein rad32	nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity DNA binding binding DNA end binding nucleic acid binding DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity DNA binding binding DNA end binding nucleic acid binding DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity DNA secondary structure binding Y-form DNA binding cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding double-stranded DNA 3'-5' DNA exonuclease activity double-stranded DNA exodeoxyribonuclease activity DNA endonuclease activity endonuclease activity single-stranded DNA endodeoxyribonuclease activity	cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair homologous recombination sexual reproduction reproductive process meiotic cell cycle process cellular component organization meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process DNA recombination meiotic cell cycle organelle fission reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process telomere organization chromosome organization telomere maintenance meiotic DNA double-strand break formation regulation of cellular process regulation of cell cycle phase transition DNA damage checkpoint signaling signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling 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 mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction regulation of cell cycle cell cycle G2/M phase transition regulation of biological process negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling 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 signal transduction in response to DNA damage negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition recombinational repair double-strand break repair via homologous recombination mitochondrial double-strand break repair mitochondrial double-strand break repair via homologous recombination mitotic intra-S DNA damage checkpoint signaling double-strand break repair involved in meiotic recombination double-strand break repair via nonhomologous end joining	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle chromosome, telomeric repeat region intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-bounded organelle protein-containing complex Mre11 complex nucleus intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle chromosome, telomeric repeat region intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-bounded organelle protein-containing complex Mre11 complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle site of double-strand break site of DNA damage
C, D	DNA repair and telomere maintenance protein nbs1	chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding binding damaged DNA binding nucleic acid binding phosphorylation-dependent protein binding protein binding modification-dependent protein binding	cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair regulation of cellular process regulation of cell cycle phase transition DNA damage checkpoint signaling signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling 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 mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling 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 regulation of biological process negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling 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 signal transduction in response to DNA damage negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition DNA recombination recombinational repair double-strand break repair via homologous recombination protein localization localization cellular localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to chromosome, telomeric region mitotic recombination telomere organization chromosome organization telomere maintenance cellular component organization organelle organization telomere maintenance via recombination cellular component organization or biogenesis mitotic intra-S DNA damage checkpoint signaling double-strand break repair via nonhomologous end joining	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure Mre11 complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure Mre11 complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle chromosome chromosome, telomeric repeat region chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR038487	Mre11, capping domain	Homologous Superfamily
A, B	IPR003701	DNA double-strand break repair protein Mre11	Family
A, B	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type	Domain
A, B	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
A, B	IPR007281	Mre11, DNA-binding	Domain
A, B	IPR041796	DNA double-strand break repair protein Mre11, N-terminal metallophosphatase domain	Domain
C, D	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
C, D	IPR000253	Forkhead-associated (FHA) domain	Domain
C, D	IPR040227	Nibrin-related	Family
C, D	IPR036420	BRCT domain superfamily	Homologous Superfamily

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.