6BZF | pdb_00006bzf

Structure of S. cerevisiae Zip2:Spo16 complex, C2 form

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	EarP	e6bzfF1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: EarP	ECOD (v294.1)
H	EarP	e6bzfH1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: EarP	ECOD (v294.1)
D	PF31229	e6bzfD1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: PF31229	ECOD (v294.1)
D	EarP	e6bzfD2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: EarP	ECOD (v294.1)
C	Spo16_C	e6bzfC2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Spo16_C	ECOD (v294.1)
G	Spo16_C	e6bzfG2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Spo16_C	ECOD (v294.1)
A	Spo16_N	e6bzfA1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Spo16_N	ECOD (v294.1)
A	Aminotran_3	e6bzfA2	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Aminotran_3	ECOD (v294.1)
E	Spo16_C	e6bzfE2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Spo16_C	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, G	PF19225	Spo16 protein, N-terminal (Spo16_N)	Spo16 protein, N-terminal	This entry represents proteins related to yeast Spo16 [1]. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA ...	This entry represents proteins related to yeast Spo16 [1]. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA structures, such as D loops and HJs [1]. The Spo16 protein contains a nuclease-like domain similar to that in ERCC1, represented in this entry, and a C-terminal HHH motif [2].	Domain
C, G	PF21698	Spo16 protein, C-terminal (Spo16_C)	Spo16 protein, C-terminal	This entry includes proteins related to yeast Spo16 [1]. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA s ...	This entry includes proteins related to yeast Spo16 [1]. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA structures, such as D loops and HJs [1]. The Spo16 protein contains a C-terminal HHH motif, represented in this entry.	Domain
A, E	PF19225	Spo16 protein, N-terminal (Spo16_N)	Spo16 protein, N-terminal	This entry represents proteins related to yeast Spo16 [1]. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA ...	This entry represents proteins related to yeast Spo16 [1]. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA structures, such as D loops and HJs [1]. The Spo16 protein contains a nuclease-like domain similar to that in ERCC1, represented in this entry, and a C-terminal HHH motif [2].	Domain
A, E	PF21698	Spo16 protein, C-terminal (Spo16_C)	Spo16 protein, C-terminal	This entry includes proteins related to yeast Spo16 [1]. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA s ...	This entry includes proteins related to yeast Spo16 [1]. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA structures, such as D loops and HJs [1]. The Spo16 protein contains a C-terminal HHH motif, represented in this entry.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, H	Protein ZIP2	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA secondary structure binding DNA binding nucleic acid binding	regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein sumoylation macromolecule modification metabolic process cellular process macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process meiotic chromosome segregation synaptonemal complex assembly cellular component biogenesis cellular component assembly synaptonemal complex organization chromosome segregation chromosome organization chromosome organization involved in meiotic cell cycle homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation regulation of cellular component organization regulation of reproductive process regulation of synaptonemal complex assembly regulation of cell cycle regulation of cell cycle process regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome SUMO ligase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome SUMO ligase complex chromosome transferase complex intracellular organelle lumen membraneless organelle condensed nuclear chromosome catalytic complex intracellular membraneless organelle synapsis initiation complex organelle lumen condensed chromosome nuclear lumen synaptonemal structure synaptonemal complex
D	Protein ZIP2	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA secondary structure binding DNA binding nucleic acid binding	regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein sumoylation macromolecule modification metabolic process cellular process macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process meiotic chromosome segregation synaptonemal complex assembly cellular component biogenesis cellular component assembly synaptonemal complex organization chromosome segregation chromosome organization chromosome organization involved in meiotic cell cycle homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation regulation of cellular component organization regulation of reproductive process regulation of synaptonemal complex assembly regulation of cell cycle regulation of cell cycle process regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome SUMO ligase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome SUMO ligase complex chromosome transferase complex intracellular organelle lumen membraneless organelle condensed nuclear chromosome catalytic complex intracellular membraneless organelle synapsis initiation complex organelle lumen condensed chromosome nuclear lumen synaptonemal structure synaptonemal complex
C, G	Sporulation-specific protein 16	DNA secondary structure binding DNA binding binding nucleic acid binding	regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein sumoylation macromolecule modification metabolic process cellular process macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process meiotic chromosome segregation synaptonemal complex assembly cellular component biogenesis cellular component assembly synaptonemal complex organization chromosome segregation chromosome organization chromosome organization involved in meiotic cell cycle homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation regulation of DNA recombination regulation of reproductive process regulation of reciprocal meiotic recombination regulation of nucleobase-containing compound metabolic process regulation of cell cycle regulation of cell cycle process regulation of DNA metabolic process developmental process sexual sporulation resulting in formation of a cellular spore cellular developmental process reproductive process in single-celled organism cell development developmental process involved in reproduction sporulation resulting in formation of a cellular spore anatomical structure morphogenesis ascospore formation sexual sporulation cell differentiation anatomical structure formation involved in morphogenesis anatomical structure development sporulation regulation of cellular component organization regulation of synaptonemal complex assembly regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome SUMO ligase complex chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome SUMO ligase complex chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle condensed nuclear chromosome catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle synapsis initiation complex organelle lumen organelle condensed chromosome nuclear lumen
B	Protein ZIP2	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA secondary structure binding DNA binding nucleic acid binding	regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein sumoylation macromolecule modification metabolic process cellular process macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process meiotic chromosome segregation synaptonemal complex assembly cellular component biogenesis cellular component assembly synaptonemal complex organization chromosome segregation chromosome organization chromosome organization involved in meiotic cell cycle homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation regulation of cellular component organization regulation of reproductive process regulation of synaptonemal complex assembly regulation of cell cycle regulation of cell cycle process regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome SUMO ligase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome SUMO ligase complex chromosome transferase complex intracellular organelle lumen membraneless organelle condensed nuclear chromosome catalytic complex intracellular membraneless organelle synapsis initiation complex organelle lumen condensed chromosome nuclear lumen synaptonemal structure synaptonemal complex
A, E	Sporulation-specific protein 16	DNA secondary structure binding DNA binding binding nucleic acid binding	regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein sumoylation macromolecule modification metabolic process cellular process macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process meiotic chromosome segregation synaptonemal complex assembly cellular component biogenesis cellular component assembly synaptonemal complex organization chromosome segregation chromosome organization chromosome organization involved in meiotic cell cycle homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation regulation of DNA recombination regulation of reproductive process regulation of reciprocal meiotic recombination regulation of nucleobase-containing compound metabolic process regulation of cell cycle regulation of cell cycle process regulation of DNA metabolic process developmental process sexual sporulation resulting in formation of a cellular spore cellular developmental process reproductive process in single-celled organism cell development developmental process involved in reproduction sporulation resulting in formation of a cellular spore anatomical structure morphogenesis ascospore formation sexual sporulation cell differentiation anatomical structure formation involved in morphogenesis anatomical structure development sporulation regulation of cellular component organization regulation of synaptonemal complex assembly regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome SUMO ligase complex chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome SUMO ligase complex chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle condensed nuclear chromosome catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle synapsis initiation complex organelle lumen organelle condensed chromosome nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, G	IPR043637	Spo16 protein, N-terminal domain	Domain
C, G	IPR048323	Spo16 protein, C-terminal	Domain
A, E	IPR043637	Spo16 protein, N-terminal domain	Domain
A, E	IPR048323	Spo16 protein, C-terminal	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
F, H	M0H	Parent Component: CYS
F, H	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084
D	M0H	Parent Component: CYS RESID: AA0075
D	MLY	Parent Component: LYS RESID: AA0075 , AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084
B	M0H	Parent Component: CYS RESID: AA0075 , AA0075
B	MLY	Parent Component: LYS RESID: AA0075 , AA0075 , AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084
A, E	MLY	Parent Component: LYS RESID: AA0075 , AA0075 , AA0075 , AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084

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.