4ZDT

Crystal structure of the RING finger domain of Slx1 in complex with the C-terminal domain of Slx4

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)
D	SCOP2 Family	Slx4 domain-like	8044991	4004239	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Slx4 domain-like	8053987	3002259	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Slx4 domain-like	8053987	3002259	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	PF21202	e4zdtA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF21202	ECOD (1.6)
C	PF21202	e4zdtC1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF21202	ECOD (1.6)
D	PF09494	e4zdtD1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF09494	ECOD (1.6)
B	PF09494	e4zdtB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF09494	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF21202	Structure-specific endonuclease subunit SLX1, C-terminal (SLX1_C)	Structure-specific endonuclease subunit SLX1, C-terminal	Slx1 is a catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. It has endonuclease activity towards branched DNA substrates, introducing single-strand ...	Slx1 is a catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. It has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA [1-3]. This is the RING zinc finger domain.	Domain
B, D	PF09494	Slx4 endonuclease (Slx4)	Slx4 endonuclease	The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearin ...	The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Structure-specific endonuclease subunit slx1	DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity double-stranded DNA endonuclease activity catalytic activity DNA nuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters crossover junction DNA endonuclease activity DNA endonuclease activity, producing 3'-phosphomonoesters 5'-flap endonuclease activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity double-stranded DNA endonuclease activity catalytic activity DNA nuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters crossover junction DNA endonuclease activity DNA endonuclease activity, producing 3'-phosphomonoesters 5'-flap endonuclease activity endodeoxyribonuclease activity, producing 5'-phosphomonoesters flap endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters ds/ssDNA junction-specific dsDNA endonuclease activity cation binding ion binding binding metal ion binding small molecule binding	DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process replication fork processing chromosome organization maintenance of DNA repeat elements DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process macromolecule metabolic process replication fork processing chromosome organization maintenance of DNA repeat elements cellular component organization maintenance of rDNA organelle organization cellular process cellular component organization or biogenesis cellular response to stimulus double-strand break repair response to stimulus DNA recombination cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle Slx1-Slx4 complex nuclear lumen non-membrane-bounded organelle nucleolar chromatin protein-DNA complex chromatin rDNA protrusion nucleolus
B, D	Structure-specific endonuclease subunit slx4	-	mitotic DNA replication DNA-templated DNA replication nuclear DNA replication cell cycle DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process mitotic cell cycle nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process mitotic cell cycle process metabolic process mitotic DNA replication DNA-templated DNA replication nuclear DNA replication cell cycle DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process mitotic cell cycle nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process mitotic cell cycle process metabolic process cellular process macromolecule metabolic process cell cycle cell cycle process DNA-templated DNA replication maintenance of fidelity replication fork processing chromosome organization maintenance of DNA repeat elements cellular component organization maintenance of rDNA organelle organization cellular component organization or biogenesis cellular response to stimulus double-strand break repair response to stimulus DNA recombination double-strand break repair via break-induced replication cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair	nucleolar chromatin membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleus membrane-enclosed lumen nuclear chromosome chromosome chromatin cellular anatomical entity intracellular membrane-bounded organelle rDNA protrusion nucleolus nucleolar chromatin membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleus membrane-enclosed lumen nuclear chromosome chromosome chromatin cellular anatomical entity intracellular membrane-bounded organelle rDNA protrusion nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nuclear protein-containing complex Slx1-Slx4 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C	IPR048749	Structure-specific endonuclease subunit SLX1, C-terminal domain	Domain
A, C	IPR027520	Structure-specific endonuclease subunit Slx1	Family
A, C	IPR035901	GIY-YIG endonuclease superfamily	Homologous Superfamily
A, C	IPR000305	GIY-YIG endonuclease	Domain
B, D	IPR018574	Structure-specific endonuclease subunit Slx4	Family

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.