5JNE | pdb_00005jne

E2-SUMO-Siz1 E3-SUMO-PCNA complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d5jneh1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	Proliferating cell nuclear antigen (PCNA)	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d5jned1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	Proliferating cell nuclear antigen (PCNA)	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
G	d5jneg_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C	d5jnec_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
F	d5jnef_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d5jneb1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d5jneb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	DNA clamp	8036430	3000780	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	DNA clamp	8036432	3000780	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA clamp	8036432	3000780	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA clamp	8036430	3000780	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	UBC-like	8061577	3000570	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	UBC-like	8061577	3000570	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	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)
H	Ribosomal_L11_N	e5jneH1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_L11_N	ECOD (v294.1)
D	Ribosomal_L11_N	e5jneD1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_L11_N	ECOD (v294.1)
G	Ribosomal_L11_N	e5jneG1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_L11_N	ECOD (v294.1)
C	Ribosomal_L11_N	e5jneC1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_L11_N	ECOD (v294.1)
F	Ribosomal_L11_N	e5jneF1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_L11_N	ECOD (v294.1)
B	Ribosomal_L11_N	e5jneB1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_L11_N	ECOD (v294.1)
A	Ribosomal_L11_N	e5jneA1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_L11_N	ECOD (v294.1)
E	Ribosomal_L11_N	e5jneE1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Ribosomal_L11_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
D	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
F	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
B	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
A	2.60.120.780	Mainly Beta	Sandwich	Jelly Rolls	PINIT domain	CATH (utative)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
E	2.60.120.780	Mainly Beta	Sandwich	Jelly Rolls	PINIT domain	CATH (utative)
E	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, H	PF02747	Proliferating cell nuclear antigen, C-terminal domain (PCNA_C)	Proliferating cell nuclear antigen, C-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
D, H	PF00705	Proliferating cell nuclear antigen, N-terminal domain (PCNA_N)	Proliferating cell nuclear antigen, N-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
C, G	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
B, F	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain
A, E	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
A, E	PF02891	MIZ/SP-RING zinc finger (zf-MIZ)	MIZ/SP-RING zinc finger	This domain has SUMO (small ubiquitin-like modifier) ligase activity and is involved in DNA repair and chromosome organisation [2][3].	Domain
A, E	PF14324	PINIT domain (PINIT)	PINIT domain	The PINIT domain is a protein domain that is found in PIAS proteins [2]. The PINIT domain is about 180 amino acids in length.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, H	Proliferating cell nuclear antigen	DNA binding binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein binding	cellular process cell cycle mitotic cell cycle DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process cellular process cell cycle mitotic cell cycle DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process leading strand elongation cellular response to stimulus response to stimulus DNA damage tolerance cellular response to stress DNA damage response response to stress mismatch repair sexual reproduction reproductive process meiotic cell cycle meiotic cell cycle process meiotic mismatch repair meiosis I cell cycle process cell cycle process DNA repair translesion synthesis nucleobase-containing compound biosynthetic process macromolecule biosynthetic process error-free translesion synthesis DNA synthesis involved in DNA replication nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization gene expression regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process mitotic sister chromatid cohesion establishment of mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion organelle organization mitotic cell cycle process establishment of sister chromatid cohesion regulation of cellular response to stress positive regulation of response to stimulus positive regulation of DNA repair regulation of response to stress regulation of DNA repair regulation of response to stimulus maintenance of DNA repeat elements maintenance of DNA trinucleotide repeats subtelomeric heterochromatin formation nucleotide-excision repair	membrane-bounded organelle protein-containing complex intracellular anatomical structure PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle enzyme activator complex DNA polymerase processivity factor complex intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork membrane-bounded organelle protein-containing complex intracellular anatomical structure PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle enzyme activator complex DNA polymerase processivity factor complex intracellular organelle cellular anatomical structure organelle membraneless organelle replication fork intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
C, G	Ubiquitin-like protein SMT3	protein tag activity molecular tag activity protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding	peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular anatomical structure cell cortex septin ring intracellular membraneless organelle intracellular organelle cell periphery cellular anatomical structure cytoskeleton organelle membraneless organelle septin cytoskeleton cytoplasm membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure cell cortex septin ring intracellular membraneless organelle intracellular organelle cell periphery cellular anatomical structure cytoskeleton organelle membraneless organelle septin cytoskeleton cytoplasm membrane-bounded organelle condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen
B, F	SUMO-conjugating enzyme UBC9	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding SUMO conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity	peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cell division peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cell division mitotic spindle elongation spindle elongation microtubule cytoskeleton organization mitotic cell cycle cellular component organization mitotic sister chromatid segregation cell cycle cellular component organization or biogenesis chromosome segregation microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process mitotic nuclear division organelle fission chromosome organization sister chromatid segregation mitotic spindle organization organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation microtubule-based process cytoskeleton organization	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
A, E	E3 SUMO-protein ligase SIZ1,Ubiquitin-like protein SMT3	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity SUMO ligase activity ubiquitin-like protein ligase activity DNA binding double-stranded DNA binding binding nucleic acid binding cation binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity SUMO ligase activity ubiquitin-like protein ligase activity DNA binding double-stranded DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding protein tag activity molecular tag activity protein binding ubiquitin-like protein ligase binding enzyme binding identical protein binding	localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope cellular process cell cycle cell cycle process negative regulation of post-translational protein modification regulation of cellular process regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination regulation of primary metabolic process localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope cellular process cell cycle cell cycle process negative regulation of post-translational protein modification regulation of cellular process regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination regulation of primary metabolic process protein ubiquitination negative regulation of protein modification process negative regulation of cellular process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal chromosome segregation peptidyl-lysine modification protein sumoylation peptidyl-amino acid modification	intracellular anatomical structure cell cortex septin ring intracellular membraneless organelle intracellular organelle cell periphery cellular anatomical structure cytoskeleton organelle membraneless organelle septin cytoskeleton cytoplasm cellular bud neck cellular bud intracellular anatomical structure cell cortex septin ring intracellular membraneless organelle intracellular organelle cell periphery cellular anatomical structure cytoskeleton organelle membraneless organelle septin cytoskeleton cytoplasm cellular bud neck cellular bud site of polarized growth chromatin chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle condensed nuclear chromosome membrane-enclosed lumen nuclear chromosome intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, H	IPR046938	DNA clamp superfamily	Homologous Superfamily
D, H	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
D, H	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
D, H	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
D, H	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
C, G	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C, G	IPR000626	Ubiquitin-like domain	Domain
C, G	IPR022617	Rad60/SUMO-like domain	Domain
B, F	IPR050113	Ubiquitin-conjugating enzyme E2-like	Family
B, F	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B, F	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
B, F	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
A, E	IPR004181	Zinc finger, MIZ-type	Domain
A, E	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, E	IPR003034	SAP domain	Domain
A, E	IPR036361	SAP domain superfamily	Homologous Superfamily
A, E	IPR031141	E3 SUMO-protein ligase SIZ1/2, SP-RING finger	Domain
A, E	IPR023321	PINIT domain	Domain
A, E	IPR038654	PINIT domain superfamily	Homologous Superfamily
A, E	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, E	IPR000626	Ubiquitin-like domain	Domain
A, E	IPR022617	Rad60/SUMO-like domain	Domain