7N0I

Structure of the SARS-CoV-2 N protein C-terminal domain bound to single-domain antibody E2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
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)
B	d7n0ib_	Alpha and beta proteins (a+b)	Nucleocapsid protein dimerization domain	Nucleocapsid protein dimerization domain	Coronavirus nucleocapsid protein	automated matches	2019-nCoV, SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],	SCOPe (2.08)
C	d7n0ic_	Alpha and beta proteins (a+b)	Nucleocapsid protein dimerization domain	Nucleocapsid protein dimerization domain	Coronavirus nucleocapsid protein	automated matches	2019-nCoV, SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],	SCOPe (2.08)
F	d7n0if_	Alpha and beta proteins (a+b)	Nucleocapsid protein dimerization domain	Nucleocapsid protein dimerization domain	Coronavirus nucleocapsid protein	automated matches	2019-nCoV, SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],	SCOPe (2.08)
G [auth H]	d7n0ih_	Alpha and beta proteins (a+b)	Nucleocapsid protein dimerization domain	Nucleocapsid protein dimerization domain	Coronavirus nucleocapsid protein	automated matches	2019-nCoV, SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],	SCOPe (2.08)
A	d7n0ia_	Alpha and beta proteins (a+b)	Nucleocapsid protein dimerization domain	Nucleocapsid protein dimerization domain	Coronavirus nucleocapsid protein	automated matches	2019-nCoV, SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],	SCOPe (2.08)
D	d7n0id_	Alpha and beta proteins (a+b)	Nucleocapsid protein dimerization domain	Nucleocapsid protein dimerization domain	Coronavirus nucleocapsid protein	automated matches	2019-nCoV, SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],	SCOPe (2.08)
E	d7n0ie_	Alpha and beta proteins (a+b)	Nucleocapsid protein dimerization domain	Nucleocapsid protein dimerization domain	Coronavirus nucleocapsid protein	automated matches	2019-nCoV, SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],	SCOPe (2.08)
L [auth G]	d7n0ig_	Alpha and beta proteins (a+b)	Nucleocapsid protein dimerization domain	Nucleocapsid protein dimerization domain	Coronavirus nucleocapsid protein	automated matches	2019-nCoV, SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ],	SCOPe (2.08)
H [auth I]	d7n0ii1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
H [auth I]	d7n0ii2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
I [auth J]	d7n0ij1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
I [auth J]	d7n0ij2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
J [auth K]	d7n0ik1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
J [auth K]	d7n0ik2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
K [auth L]	d7n0il1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
K [auth L]	d7n0il2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleocapsid protein dimerization domain	8092722	3001606	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleocapsid protein dimerization domain	8092722	3001606	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nucleocapsid protein dimerization domain	8092722	3001606	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	Nucleocapsid protein dimerization domain	8092722	3001606	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleocapsid protein dimerization domain	8092722	3001606	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleocapsid protein dimerization domain	8092722	3001606	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleocapsid protein dimerization domain	8092722	3001606	SCOP2B (2022-06-29)
L [auth G]	SCOP2B Superfamily	Nucleocapsid protein dimerization domain	8092722	3001606	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)
B	PF00937	e7n0iB1	A: a+b duplicates or obligate multimers	X: Arterivirus nucleocapsid protein (From Topology)	H: Arterivirus nucleocapsid protein (From Topology)	T: Arterivirus nucleocapsid protein	F: PF00937	ECOD (1.6)
C	PF00937	e7n0iC1	A: a+b duplicates or obligate multimers	X: Arterivirus nucleocapsid protein (From Topology)	H: Arterivirus nucleocapsid protein (From Topology)	T: Arterivirus nucleocapsid protein	F: PF00937	ECOD (1.6)
F	PF00937	e7n0iF1	A: a+b duplicates or obligate multimers	X: Arterivirus nucleocapsid protein (From Topology)	H: Arterivirus nucleocapsid protein (From Topology)	T: Arterivirus nucleocapsid protein	F: PF00937	ECOD (1.6)
G [auth H]	PF00937	e7n0iH1	A: a+b duplicates or obligate multimers	X: Arterivirus nucleocapsid protein (From Topology)	H: Arterivirus nucleocapsid protein (From Topology)	T: Arterivirus nucleocapsid protein	F: PF00937	ECOD (1.6)
A	PF00937	e7n0iA1	A: a+b duplicates or obligate multimers	X: Arterivirus nucleocapsid protein (From Topology)	H: Arterivirus nucleocapsid protein (From Topology)	T: Arterivirus nucleocapsid protein	F: PF00937	ECOD (1.6)
D	PF00937	e7n0iD1	A: a+b duplicates or obligate multimers	X: Arterivirus nucleocapsid protein (From Topology)	H: Arterivirus nucleocapsid protein (From Topology)	T: Arterivirus nucleocapsid protein	F: PF00937	ECOD (1.6)
E	PF00937	e7n0iE1	A: a+b duplicates or obligate multimers	X: Arterivirus nucleocapsid protein (From Topology)	H: Arterivirus nucleocapsid protein (From Topology)	T: Arterivirus nucleocapsid protein	F: PF00937	ECOD (1.6)
L [auth G]	PF00937	e7n0iG1	A: a+b duplicates or obligate multimers	X: Arterivirus nucleocapsid protein (From Topology)	H: Arterivirus nucleocapsid protein (From Topology)	T: Arterivirus nucleocapsid protein	F: PF00937	ECOD (1.6)
H [auth I]	PF07686	e7n0iI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I [auth J]	PF07686	e7n0iJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
J [auth K]	PF07686	e7n0iK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
K [auth L]	PF07686	e7n0iL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
H [auth I], I [auth J], J [auth K], K [auth L]	Heavy Chain	IGHV1	-	nucleoprotein \| nucleoprotein	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E, A, B, C, D, E, F, G [auth H], L [auth G]	PF00937	Coronavirus nucleocapsid (CoV_nucleocap)	Coronavirus nucleocapsid	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E, A, B, C, D, E, F, G [auth H], L [auth G]	Nucleoprotein	molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity molecular sequestering activity protein sequestering activity RNA binding binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity RNA stem-loop binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity molecular sequestering activity protein sequestering activity RNA binding binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity RNA stem-loop binding MHC class I protein binding signaling receptor binding MHC protein binding	response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism 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 response to host immune response response to host response to external biotic stimulus multicellular organismal process regulation of cellular process response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism 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 response to host immune response response to host response to external biotic stimulus multicellular organismal process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of type I interferon production organic substance metabolic process cytokine production organic substance biosynthetic process negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process regulation of interferon-beta production interferon-beta production negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process type I interferon production cellular metabolic process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of interferon-beta production metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production cellular response to stimulus positive regulation of cell communication positive regulation of response to biotic stimulus positive regulation of signal transduction pattern recognition receptor signaling pathway regulation of NLRP3 inflammasome complex assembly positive regulation of NLRP3 inflammasome complex assembly regulation of signal transduction cell communication cellular component biogenesis immune response-activating signaling pathway cellular component assembly inflammasome-mediated signaling pathway positive regulation of immune response canonical inflammasome complex assembly regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway immune response regulation of innate immune response positive regulation of inflammasome-mediated signaling pathway regulation of inflammasome-mediated signaling pathway regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway NLRP3 inflammasome complex assembly positive regulation of defense response activation of innate immune response regulation of immune response inflammatory response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus regulation of cellular component organization positive regulation of cellular component organization regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process regulation of cytoplasmic pattern recognition receptor signaling pathway positive regulation of response to stimulus cellular component organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response protein-containing complex assembly cellular component organization or biogenesis positive regulation of cellular process regulation of signaling positive regulation of innate immune response defense response protein-containing complex organization positive regulation of cellular component biogenesis defense response to symbiont regulation of cellular component biogenesis immune system process regulation of cell communication positive regulation of signaling virion assembly cytoplasmic capsid assembly viral process viral capsid assembly viral life cycle viral RNA genome packaging viral genome packaging	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle host extracellular space viral capsid virion component intracellular organelle host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle host extracellular space viral capsid virion component intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle MHC class I protein complex MHC protein complex cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cytoplasm host cell perinuclear region of cytoplasm extracellular region host cell Golgi apparatus ribonucleoprotein complex viral nucleocapsid
H [auth I], I [auth J], J [auth K], K [auth L]	Single-domain antibody E2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E, A, B, C, D, E, F, G [auth H], L [auth G]	IPR044344	Nucleocapsid (N) protein, C-terminal domain, coronavirus	Domain
A, B, C, D, E, A, B, C, D, E, F, G [auth H], L [auth G]	IPR043505	Nucleocapsid protein, betacoronavirus	Family
A, B, C, D, E, A, B, C, D, E, F, G [auth H], L [auth G]	IPR001218	Nucleocapsid protein, coronavirus	Family
A, B, C, D, E, A, B, C, D, E, F, G [auth H], L [auth G]	IPR037195	Nucleocapsid protein, N-terminal	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G [auth H], L [auth G]	IPR037179	Nucleocapsid protein, C-terminal	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G [auth H], L [auth G]	IPR044345	Nucleocapsid (N) protein, N-terminal domain, coronavirus	Domain

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.