7BU8 | pdb_00007bu8

Cryo-EM structure of zika virus complexed with Fab SIgN-3C at pH 6.5


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyE set domains 8073018 3000070 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyE set domains 8073018 3000070 SCOP2B (2022-06-29)
D [auth B]SCOP2B SuperfamilyE set domains 8073018 3000070 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
H [auth I]C1-sete7bu8I1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: C1-setECOD (v294.1)
J [auth L]Flavi_Me7bu8L1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_MECOD (v294.1)
L [auth K]Flavi_Me7bu8K1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_MECOD (v294.1)
GC1-sete7bu8G1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: C1-setECOD (v294.1)
I [auth H]Flavi_Me7bu8H1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_MECOD (v294.1)
K [auth J]Flavi_Me7bu8J1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_MECOD (v294.1)
EFlavi_Me7bu8E1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_MECOD (v294.1)
FFlavi_Me7bu8F1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_MECOD (v294.1)
C [auth D]C1-sete7bu8D1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: C1-setECOD (v294.1)
AC1-sete7bu8A1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: C1-setECOD (v294.1)
B [auth C]Flavi_Me7bu8C1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_MECOD (v294.1)
D [auth B]Flavi_Me7bu8B1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_MECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
E1.10.8.970 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (utative)
F1.10.8.970 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (utative)
C [auth D]1.10.8.970 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3CATH (utative)
A2.60.98.10 Mainly Beta Sandwich Tick-borne Encephalitis virus Glycoprotein domain 1CATH (utative)
A3.30.67.10 Alpha Beta 2-Layer Sandwich Viral Envelope Glycoprotein domain 2CATH (utative)
A3.30.387.10 Alpha Beta 2-Layer Sandwich Viral Envelope Glycoprotein domain 3CATH (utative)
A2.60.40.350 Mainly Beta Sandwich Immunoglobulin-like CATH (utative)
A1.20.1280.260 Mainly Alpha Up-down Bundle Monooxygenase CATH (utative)
B [auth C]2.60.98.10 Mainly Beta Sandwich Tick-borne Encephalitis virus Glycoprotein domain 1CATH (utative)
B [auth C]3.30.67.10 Alpha Beta 2-Layer Sandwich Viral Envelope Glycoprotein domain 2CATH (utative)
B [auth C]3.30.387.10 Alpha Beta 2-Layer Sandwich Viral Envelope Glycoprotein domain 3CATH (utative)
B [auth C]2.60.40.350 Mainly Beta Sandwich Immunoglobulin-like CATH (utative)
B [auth C]1.20.1280.260 Mainly Alpha Up-down Bundle Monooxygenase CATH (utative)
D [auth B]2.60.98.10 Mainly Beta Sandwich Tick-borne Encephalitis virus Glycoprotein domain 1CATH (utative)
D [auth B]3.30.67.10 Alpha Beta 2-Layer Sandwich Viral Envelope Glycoprotein domain 2CATH (utative)
D [auth B]3.30.387.10 Alpha Beta 2-Layer Sandwich Viral Envelope Glycoprotein domain 3CATH (utative)
D [auth B]2.60.40.350 Mainly Beta Sandwich Immunoglobulin-like CATH (utative)
D [auth B]1.20.1280.260 Mainly Alpha Up-down Bundle Monooxygenase CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
H [auth I],
J [auth L],
L [auth K]
Fab SIgN-3C, anti-DEN, neutralizing V-KAPPA Homo sapiens (human) IGKV1-33*01, IGKV1D-33*01, IGKJ5*01 V-DOMAIN V-KAPPA IG FV-HEAVY_KAPPA IMGT (202613-0)
G,
I [auth H],
K [auth J]
Fab SIgN-3C, anti-DEN, neutralizing VH Homo sapiens (human) IGHV1-46*01, IGHV1-46*03, IGHJ5*02 V-DOMAIN VH IG FV-HEAVY_KAPPA IMGT (202613-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
H [auth I],
J [auth L],
L [auth K]
Light ChainIGKV1 Kappagenome polyproteinSAbDab (2026-04-10)
G,
I [auth H],
K [auth J]
Heavy ChainIGHV1 -genome polyproteinSAbDab (2026-04-10)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
H [auth I],
J [auth L],
L [auth K]
SIgN-3C Fab light chain---
G,
I [auth H],
K [auth J]
SIgN-3C Fab heavy chain---
C [auth D],
E,
F
Zika virus M protein
A,
B [auth C],
D [auth B]
Genome polyprotein

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
C [auth D],
E,
F
IPR000208RNA-directed RNA polymerase, fingers/palm subdomains, flavivirusDomain
C [auth D],
E,
F
IPR014756Immunoglobulin E-setHomologous Superfamily
C [auth D],
E,
F
IPR001122Capsid protein C, flavivirusDomain
C [auth D],
E,
F
IPR027287Glycoprotein E, immunoglobulin-like domain, flavivirusDomain
C [auth D],
E,
F
IPR014412Genome polyprotein, FlavivirusFamily
C [auth D],
E,
F
IPR036253Flavivirus glycoprotein, central and dimerisation domain superfamilyHomologous Superfamily
C [auth D],
E,
F
IPR011492Non-structural protein NS3-like, DEAD-box helicase, flavivirusDomain
C [auth D],
E,
F
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
C [auth D],
E,
F
IPR026490mRNA cap 0/1 methyltransferaseDomain
C [auth D],
E,
F
IPR009003Peptidase S1, PA clanHomologous Superfamily
C [auth D],
E,
F
IPR001650Helicase, C-terminal domain-likeDomain
C [auth D],
E,
F
IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
C [auth D],
E,
F
IPR013755Flaviviral glycoprotein E, central domain, subdomain 1Homologous Superfamily
C [auth D],
E,
F
IPR000752Flavivirus non-structural protein NS2ADomain
C [auth D],
E,
F
IPR047530RNA-dependent RNA polymerase, flavivirusDomain
C [auth D],
E,
F
IPR049486Flavivridae NS3 helicase, C-terminal helical domainDomain
C [auth D],
E,
F
IPR046811RNA-directed RNA polymerase, thumb subdomain, flavivirusDomain
C [auth D],
E,
F
IPR038055Flaviviral glycoprotein E, dimerisation domainHomologous Superfamily
C [auth D],
E,
F
IPR002877Ribosomal RNA methyltransferase, FtsJ domainDomain
C [auth D],
E,
F
IPR038302Envelope glycoprotein M superfamily, flavivirusHomologous Superfamily
C [auth D],
E,
F
IPR000069Envelope glycoprotein M, flavivirusDomain
C [auth D],
E,
F
IPR038345Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamilyHomologous Superfamily
C [auth D],
E,
F
IPR038688Flavivirus polyprotein propeptide superfamilyHomologous Superfamily
C [auth D],
E,
F
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
C [auth D],
E,
F
IPR026470Flavivirus envelope glycoprotein E, Stem/Anchor domainDomain
C [auth D],
E,
F
IPR011998Envelope glycoprotein E, central and dimerisation domain, flavivirusDomain
C [auth D],
E,
F
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
C [auth D],
E,
F
IPR037172Flavivirus capsid protein C superfamilyHomologous Superfamily
C [auth D],
E,
F
IPR000404Flavivirus non-structural protein NS4ADomain
C [auth D],
E,
F
IPR000487Non-structural protein NS2B, flavivirusDomain
C [auth D],
E,
F
IPR001528Flavivirus non-structural protein NS4BDomain
C [auth D],
E,
F
IPR001157Non-structural protein NS1, flavivirusDomain
C [auth D],
E,
F
IPR013756Flaviviral glycoprotein E, central domain, subdomain 2Homologous Superfamily
C [auth D],
E,
F
IPR001850Non-structural protein NS3, peptidase S7, flavivirusDomain
C [auth D],
E,
F
IPR000336Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamilyHomologous Superfamily
C [auth D],
E,
F
IPR002535Flavivirus polyprotein propeptideDomain
C [auth D],
E,
F
IPR007094RNA-directed RNA polymerase, catalytic domainDomain
A,
B [auth C],
D [auth B]
IPR000208RNA-directed RNA polymerase, fingers/palm subdomains, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR014756Immunoglobulin E-setHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR001122Capsid protein C, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR027287Glycoprotein E, immunoglobulin-like domain, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR014412Genome polyprotein, FlavivirusFamily
A,
B [auth C],
D [auth B]
IPR036253Flavivirus glycoprotein, central and dimerisation domain superfamilyHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR011492Non-structural protein NS3-like, DEAD-box helicase, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR026490mRNA cap 0/1 methyltransferaseDomain
A,
B [auth C],
D [auth B]
IPR009003Peptidase S1, PA clanHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR001650Helicase, C-terminal domain-likeDomain
A,
B [auth C],
D [auth B]
IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
A,
B [auth C],
D [auth B]
IPR013755Flaviviral glycoprotein E, central domain, subdomain 1Homologous Superfamily
A,
B [auth C],
D [auth B]
IPR000752Flavivirus non-structural protein NS2ADomain
A,
B [auth C],
D [auth B]
IPR047530RNA-dependent RNA polymerase, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR049486Flavivridae NS3 helicase, C-terminal helical domainDomain
A,
B [auth C],
D [auth B]
IPR046811RNA-directed RNA polymerase, thumb subdomain, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR038055Flaviviral glycoprotein E, dimerisation domainHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR002877Ribosomal RNA methyltransferase, FtsJ domainDomain
A,
B [auth C],
D [auth B]
IPR038302Envelope glycoprotein M superfamily, flavivirusHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR000069Envelope glycoprotein M, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR038345Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamilyHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR038688Flavivirus polyprotein propeptide superfamilyHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR026470Flavivirus envelope glycoprotein E, Stem/Anchor domainDomain
A,
B [auth C],
D [auth B]
IPR011998Envelope glycoprotein E, central and dimerisation domain, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR037172Flavivirus capsid protein C superfamilyHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR000404Flavivirus non-structural protein NS4ADomain
A,
B [auth C],
D [auth B]
IPR000487Non-structural protein NS2B, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR001528Flavivirus non-structural protein NS4BDomain
A,
B [auth C],
D [auth B]
IPR001157Non-structural protein NS1, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR013756Flaviviral glycoprotein E, central domain, subdomain 2Homologous Superfamily
A,
B [auth C],
D [auth B]
IPR001850Non-structural protein NS3, peptidase S7, flavivirusDomain
A,
B [auth C],
D [auth B]
IPR000336Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamilyHomologous Superfamily
A,
B [auth C],
D [auth B]
IPR002535Flavivirus polyprotein propeptideDomain
A,
B [auth C],
D [auth B]
IPR007094RNA-directed RNA polymerase, catalytic domainDomain