7R98

Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody B6

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)
D	d7r98d_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d7r98e1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d7r98e2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d7r98f1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d7r98f2	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)
A	SCOP2B Superfamily	SARS coronavirus nucleoprotein RNA-binding domain-like	8092433	3000498	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SARS coronavirus nucleoprotein RNA-binding domain-like	8092433	3000498	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SARS coronavirus nucleoprotein RNA-binding domain-like	8092433	3000498	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	Corona_nucleoca_1st	e7r98A1	A: beta complex topology	X: Coronavirus RNA-binding domain (N-terminal part of Pfam 00937) (From Topology)	H: Coronavirus RNA-binding domain (N-terminal part of Pfam 00937) (From Topology)	T: Coronavirus RNA-binding domain (N-terminal part of Pfam 00937)	F: Corona_nucleoca_1st	ECOD (1.6)
B	Corona_nucleoca_1st	e7r98B1	A: beta complex topology	X: Coronavirus RNA-binding domain (N-terminal part of Pfam 00937) (From Topology)	H: Coronavirus RNA-binding domain (N-terminal part of Pfam 00937) (From Topology)	T: Coronavirus RNA-binding domain (N-terminal part of Pfam 00937)	F: Corona_nucleoca_1st	ECOD (1.6)
C	Corona_nucleoca_1st	e7r98C1	A: beta complex topology	X: Coronavirus RNA-binding domain (N-terminal part of Pfam 00937) (From Topology)	H: Coronavirus RNA-binding domain (N-terminal part of Pfam 00937) (From Topology)	T: Coronavirus RNA-binding domain (N-terminal part of Pfam 00937)	F: Corona_nucleoca_1st	ECOD (1.6)
D	V-set_8	e7r98D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E	V-set_8	e7r98E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F	V-set_8	e7r98F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D, E, F	Heavy Chain	IGHV1	-	nucleoprotein	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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	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 negative regulation of biological process negative regulation of type I interferon production cytokine production 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 negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule 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 intracellular 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 intracellular signal transduction 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 intracellular signal transduction 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 cellular anatomical structure host cell cytoplasm host cell part host intracellular region 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 cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell cytoplasm part host intracellular organelle host extracellular space viral capsid virion component intracellular organelle intracellular anatomical structure organelle membraneless organelle intracellular membraneless 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
D, E, F	Nanobody B6	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR044344	Nucleocapsid (N) protein, C-terminal domain, coronavirus	Domain
A, B, C	IPR043505	Nucleocapsid protein, betacoronavirus	Family
A, B, C	IPR001218	Nucleocapsid protein, coronavirus	Family
A, B, C	IPR037195	Nucleocapsid protein, N-terminal	Homologous Superfamily
A, B, C	IPR037179	Nucleocapsid protein, C-terminal	Homologous Superfamily
A, B, C	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 R01GM157729.