6PW2

Structural Basis for Cooperative Binding of EBNA1 to the Epstein-Barr Virus Dyad Symmetry Minimal Origin of Replication

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)
G [auth I]	SCOP2B Superfamily	Viral DNA-binding domain	8035383	3001239	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	Viral DNA-binding domain	8035383	3001239	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Viral DNA-binding domain	8035383	3001239	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Viral DNA-binding domain	8035383	3001239	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Viral DNA-binding domain	8035383	3001239	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Viral DNA-binding domain	8035383	3001239	SCOP2B (2022-06-29)
H [auth J]	SCOP2B Superfamily	Viral DNA-binding domain	8035383	3001239	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	Viral DNA-binding domain	8035383	3001239	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)
G [auth I]	EBV-NA1	e6pw2I1	A: a+b two layers	X: Alpha-beta plaits	H: Viral DNA-binding domain (From Topology)	T: Viral DNA-binding domain	F: EBV-NA1	ECOD (1.6)
I [auth K]	EBV-NA1	e6pw2K1	A: a+b two layers	X: Alpha-beta plaits	H: Viral DNA-binding domain (From Topology)	T: Viral DNA-binding domain	F: EBV-NA1	ECOD (1.6)
A	EBV-NA1	e6pw2A1	A: a+b two layers	X: Alpha-beta plaits	H: Viral DNA-binding domain (From Topology)	T: Viral DNA-binding domain	F: EBV-NA1	ECOD (1.6)
B	EBV-NA1	e6pw2B1	A: a+b two layers	X: Alpha-beta plaits	H: Viral DNA-binding domain (From Topology)	T: Viral DNA-binding domain	F: EBV-NA1	ECOD (1.6)
C	EBV-NA1	e6pw2C1	A: a+b two layers	X: Alpha-beta plaits	H: Viral DNA-binding domain (From Topology)	T: Viral DNA-binding domain	F: EBV-NA1	ECOD (1.6)
D	EBV-NA1	e6pw2D1	A: a+b two layers	X: Alpha-beta plaits	H: Viral DNA-binding domain (From Topology)	T: Viral DNA-binding domain	F: EBV-NA1	ECOD (1.6)
H [auth J]	EBV-NA1	e6pw2J1	A: a+b two layers	X: Alpha-beta plaits	H: Viral DNA-binding domain (From Topology)	T: Viral DNA-binding domain	F: EBV-NA1	ECOD (1.6)
J [auth L]	EBV-NA1	e6pw2L1	A: a+b two layers	X: Alpha-beta plaits	H: Viral DNA-binding domain (From Topology)	T: Viral DNA-binding domain	F: EBV-NA1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G [auth I]	3.30.70.390	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Epstein Barr virus nuclear antigen-1, DNA-binding domain	CATH (utative)
I [auth K]	3.30.70.390	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Epstein Barr virus nuclear antigen-1, DNA-binding domain	CATH (utative)
A	3.30.70.390	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Epstein Barr virus nuclear antigen-1, DNA-binding domain	CATH (utative)
B	3.30.70.390	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Epstein Barr virus nuclear antigen-1, DNA-binding domain	CATH (utative)
C	3.30.70.390	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Epstein Barr virus nuclear antigen-1, DNA-binding domain	CATH (utative)
D	3.30.70.390	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Epstein Barr virus nuclear antigen-1, DNA-binding domain	CATH (utative)
H [auth J]	3.30.70.390	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Epstein Barr virus nuclear antigen-1, DNA-binding domain	CATH (utative)
J [auth L]	3.30.70.390	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Epstein Barr virus nuclear antigen-1, DNA-binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, G [auth I], A, B, C, D, G [auth I], H [auth J], I [auth K], J [auth L]	PF02905	Epstein Barr virus nuclear antigen-1, DNA-binding domain (EBV-NA1)	Epstein Barr virus nuclear antigen-1, DNA-binding domain	This domain has a ferredoxin-like fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, G [auth I], A, B, C, D, G [auth I], H [auth J], I [auth K], J [auth L]	Epstein-Barr nuclear antigen 1	DNA binding binding organic cyclic compound binding nucleic acid binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity transcription regulator activity DNA-binding transcription factor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response modulation by symbiont of host process response to host immune response symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response modulation by symbiont of host process response to host immune response symbiont-mediated suppression of host antigen processing and presentation response to host response to external biotic stimulus modulation of process of another organism symbiont-mediated suppression of host adaptive immune response symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cell PML body symbiont-mediated disruption of host cellular anatomical entity disruption of anatomical structure in another organism viral latency viral process regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process cellular process positive regulation of cellular biosynthetic process DNA metabolic process DNA replication regulation of DNA replication regulation of DNA metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell part host intracellular region cellular anatomical entity host cell nucleus host cell nuclear part host cell PML body host intracellular organelle
E, K [auth G]	DNA (62-MER)	-	-	-
F, L [auth H]	DNA (62-MER) complementary DNA strand	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, G [auth I], A, B, C, D, G [auth I], H [auth J], I [auth K], J [auth L]	IPR004186	Epstein Barr virus nuclear antigen-1, DNA-binding	Domain
A, B, C, D, G [auth I], A, B, C, D, G [auth I], H [auth J], I [auth K], J [auth L]	IPR035975	E2/EBNA1, C-terminal	Homologous Superfamily
A, B, C, D, G [auth I], A, B, C, D, G [auth I], H [auth J], I [auth K], J [auth L]	IPR037007	Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily	Homologous Superfamily

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.