3T1I

Crystal Structure of Human Mre11: Understanding Tumorigenic Mutations

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)
C	SCOP2 Family	Mre11-like	8045458	4003657	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Metallo-dependent phosphatases	8090756	3001067	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Mre11 C-terminal domain-like	8090757	3002453	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Metallo-dependent phosphatases	8090756	3001067	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Mre11 C-terminal domain-like	8090757	3002453	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mre11 C-terminal domain-like	8090757	3002453	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-dependent phosphatases	8090756	3001067	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent phosphatases	8090756	3001067	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Mre11 C-terminal domain-like	8090757	3002453	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)
C	Metallophos_2_1	e3t1iC2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
C	Mre11_DNA_bind_N	e3t1iC1	A: a+b four layers	X: Mre11 nuclease C-terminal domain (From Topology)	H: Mre11 nuclease C-terminal domain (From Topology)	T: Mre11 nuclease C-terminal domain	F: Mre11_DNA_bind_N	ECOD (1.6)
D	Metallophos_2_1	e3t1iD1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
D	Mre11_DNA_bind_N	e3t1iD2	A: a+b four layers	X: Mre11 nuclease C-terminal domain (From Topology)	H: Mre11 nuclease C-terminal domain (From Topology)	T: Mre11 nuclease C-terminal domain	F: Mre11_DNA_bind_N	ECOD (1.6)
A	Metallophos_2_1	e3t1iA2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
A	Mre11_DNA_bind_N	e3t1iA1	A: a+b four layers	X: Mre11 nuclease C-terminal domain (From Topology)	H: Mre11 nuclease C-terminal domain (From Topology)	T: Mre11 nuclease C-terminal domain	F: Mre11_DNA_bind_N	ECOD (1.6)
B	Metallophos_2_1	e3t1iB2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2_1	ECOD (1.6)
B	Mre11_DNA_bind_N	e3t1iB1	A: a+b four layers	X: Mre11 nuclease C-terminal domain (From Topology)	H: Mre11 nuclease C-terminal domain (From Topology)	T: Mre11 nuclease C-terminal domain	F: Mre11_DNA_bind_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
C	3.30.110.110	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	Mre11, capping domain	CATH (4.3.0)
D	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
D	3.30.110.110	Alpha Beta	2-Layer Sandwich	Translation Initiation Factor IF3	Mre11, capping domain	CATH (4.3.0)
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, C, D	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, C, D	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 i ...	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, C, D	Double-strand break repair protein MRE11A	nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding 5'-3' exonuclease activity exonuclease activity 3'-5' exonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding 5'-3' exonuclease activity exonuclease activity 3'-5' exonuclease activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid single-stranded DNA endodeoxyribonuclease activity DNA nuclease activity cell adhesion molecule binding cadherin binding protein binding identical protein binding DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 3'-5'-DNA exonuclease activity DNA binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process double-strand break repair DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process double-strand break repair DNA double-strand break processing primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic 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 cell population proliferation chromosome organization sister chromatid cohesion regulation of cellular process positive regulation of phosphorylation regulation of catalytic activity positive regulation of biological process positive regulation of cellular metabolic process regulation of transferase activity positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of molecular function regulation of phosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process positive regulation of cellular process regulation of biological process positive regulation of transferase activity positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process biological regulation positive regulation of catalytic activity regulation of cellular metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of phosphorylation regulation of phosphorus metabolic process regulation of metabolic process DNA duplex unwinding DNA geometric change DNA conformation change mitochondrial double-strand break repair mitochondrial double-strand break repair via homologous recombination recombinational repair positive regulation of organelle organization regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization telomere organization regulation of primary metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of telomere maintenance positive regulation of nucleobase-containing compound metabolic process regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization positive regulation of chromosome organization telomere maintenance positive regulation of DNA metabolic process regulation of DNA metabolic process DNA damage checkpoint signaling regulation of cell cycle phase transition 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 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 mitotic intra-S DNA damage checkpoint signaling regulation of cell cycle regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling mitotic cell cycle process signal transduction in response to DNA damage G2/M transition of mitotic cell cycle mitotic G2/M transition checkpoint 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 G2/M phase transition regulation of mitotic cell cycle phase transition negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition 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 nucleobase-containing compound biosynthetic process macromolecule biosynthetic process biosynthetic process organic cyclic compound biosynthetic process DNA biosynthetic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death meiotic chromosome segregation chromosome organization involved in meiotic cell cycle homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation chromosome segregation telomeric 3' overhang formation DNA strand elongation telomere capping meiotic DNA double-strand break formation regulation of DNA recombination mitotic recombination regulation of mitotic recombination DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA replication DNA strand resection involved in replication fork processing replication fork processing mitotic G2 DNA damage checkpoint signaling double-strand break repair via homologous recombination regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of protein modification process protein metabolic process positive regulation of protein phosphorylation protein modification process organonitrogen compound metabolic process protein phosphorylation protein autophosphorylation regulation of protein metabolic process regulation of protein autophosphorylation macromolecule modification positive regulation of protein autophosphorylation double-strand break repair via nonhomologous end joining	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure BRCA1-C complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity cytoplasm cytosol intracellular non-membrane-bounded organelle chromosome membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure BRCA1-C complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity cytoplasm cytosol intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region chromosomal region non-membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen 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	IPR041796	Mre11 nuclease, N-terminal metallophosphatase domain	Domain
A, B, C, D	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type	Domain
A, B, C, D	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
A, B, C, D	IPR038487	Mre11, capping domain	Homologous Superfamily
A, B, C, D	IPR003701	DNA double-strand break repair protein Mre11	Family
A, B, C, D	IPR007281	Mre11, DNA-binding	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P49959	ataxia-telangiectasia-like disorder 1 microcephaly osteosarcoma ataxia-telangiectasia-like disorder ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia BAP1-related tumor predisposition syndrome hereditary breast carcinoma intellectual disability malignant colon neoplasm Malignant neoplasm of ovary Nijmegen breakage syndrome-like disorder cancer hereditary breast ovarian cancer syndrome large cell medulloblastoma malignant ependymoma ataxia-telangiectasia-like disorder 1 microcephaly osteosarcoma ataxia-telangiectasia-like disorder ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia BAP1-related tumor predisposition syndrome hereditary breast carcinoma intellectual disability malignant colon neoplasm Malignant neoplasm of ovary Nijmegen breakage syndrome-like disorder cancer hereditary breast ovarian cancer syndrome large cell medulloblastoma malignant ependymoma medulloblastoma obstructive sleep apnea syndrome atypical teratoid rhabdoid tumor Charcot-Marie-Tooth disease hereditary hemorrhagic telangiectasia lung cancer

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.