4Y66 | pdb_00004y66

Crystal structure of Giardia lamblia Hop2-Mnd1 complex

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)
F	SCOP2 Family	Hop2 N-terminal domain-like	8049070	4006330	SCOP2 (2022-06-29)
F	SCOP2 Family	Hop2 coiled coil region-like	8089882	4007689	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Winged helix DNA-binding domain	8089881	3000034	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Mnd1/Hop2-like	8089883	3002398	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8089881	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Mnd1/Hop2-like	8089883	3002398	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Mnd1/Hop2-like	8089883	3002398	SCOP2B (2022-06-29)
E	SCOP2 Family	Mnd1 N-terminal domain-like	8045250	4004373	SCOP2 (2022-06-29)
E	SCOP2 Family	Mnd1 coiled coil region-like	8089879	4007688	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Winged helix DNA-binding domain	8089878	3000034	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Mnd1/Hop2-like	8089880	3002398	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Mnd1/Hop2-like	8089880	3002398	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8089878	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mnd1/Hop2-like	8089880	3002398	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)
F	TBPIP	e4y66F1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: TBPIP	ECOD (1.6)
D	TBPIP	e4y66D1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: TBPIP	ECOD (1.6)
E	Mnd1	e4y66E1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Mnd1	ECOD (1.6)
C	Mnd1	e4y66C1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Mnd1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF18517	Leucine zipper with capping helix domain (LZ3wCH)	Leucine zipper with capping helix domain	This domain is found at the C-terminal region of Hop2 and Mnd1 proteins. In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex. Hop2 (fo ...	This domain is found at the C-terminal region of Hop2 and Mnd1 proteins. In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex. Hop2 (for homologous pairing; also known as TBPIP) is expressed specifically during meiosis, same as Mnd1 (for meiotic nuclear divisions 1). The C-terminal region of both Hop2 and Mnd1, folds into three alpha-helices that are interrupted by two short non-helical regions. These alpha-helices of the two proteins together form a parallel coiled coil that provides the major interface for heterodimer formation. The non-helical regions form substantially kinked junctions between adjacent leucine zippers: the LZ1-LZ2 and LZ2-LZ3 junctions.This domain is the C-terminal segment of Hop2 and Mnd1 which folds back onto the C-terminal leucine zipper (LZ3) to form a helical bundle-like structure, hence designated LZ3wCH (for LZ3 with capping helices). The LZ3wCH region plays a role in interacting with the Dmc1 nucleofilament [1].	Domain
A, C, E	PF03962	Mnd1 HTH domain (Mnd1)	Mnd1 HTH domain	This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	Putative tbpip family protein	DNA binding double-stranded DNA binding binding nucleic acid binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity recombinase activator activity	sexual reproduction homologous recombination reproductive process meiotic cell cycle process nucleobase-containing compound metabolic process cellular component organization meiosis I meiotic strand invasion meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process meiotic cell cycle sexual reproduction homologous recombination reproductive process meiotic cell cycle process nucleobase-containing compound metabolic process cellular component organization meiosis I meiotic strand invasion meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process meiotic cell cycle DNA recombination organelle fission primary metabolic process DNA metabolic process meiotic strand invasion involved in reciprocal meiotic recombination DNA strand invasion nucleic acid metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process cellular process metabolic process macromolecule metabolic process meiotic chromosome segregation chromosome organization chromosome organization involved in meiotic cell cycle homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation chromosome segregation meiotic joint molecule formation	membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle condensed chromosome nuclear lumen protein-containing complex DNA recombinase auxiliary factor complex enzyme activator complex
A, C, E	Mnd1	DNA binding double-stranded DNA binding binding nucleic acid binding	homologous recombination sexual reproduction reproductive process meiotic cell cycle process nucleobase-containing compound metabolic 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 homologous recombination sexual reproduction reproductive process meiotic cell cycle process nucleobase-containing compound metabolic 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 primary metabolic process DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR010776	Homologous-pairing protein 2, winged helix domain	Domain
B, D, F	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, C, E	IPR040661	Leucine zipper with capping helix domain	Domain
A, C, E	IPR005647	Meiotic nuclear division protein 1	Family
A, C, E	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, C, E	IPR040453	Mnd1, HTH domain	Domain
A, C, E	IPR036390	Winged helix DNA-binding 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.