6IDK | pdb_00006idk

Cryo-EM structure of Immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 5.0 (Class I particle)


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AFlavi_glycop_Ce6idkA1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_glycop_CECOD (1.6)
AFlavi_glycoprote6idkA2 A: beta complex topologyX: Viral glycoprotein, central and dimerisation domains-likeH: Viral glycoprotein, central and dimerisation domains (From Topology)T: Viral glycoprotein, central and dimerisation domainsF: Flavi_glycoprotECOD (1.6)
BFlavi_glycop_Ce6idkB2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_glycop_CECOD (1.6)
BFlavi_glycoprote6idkB1 A: beta complex topologyX: Viral glycoprotein, central and dimerisation domains-likeH: Viral glycoprotein, central and dimerisation domains (From Topology)T: Viral glycoprotein, central and dimerisation domainsF: Flavi_glycoprotECOD (1.6)
CFlavi_glycop_Ce6idkC1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Flavi_glycop_CECOD (1.6)
CFlavi_glycoprote6idkC2 A: beta complex topologyX: Viral glycoprotein, central and dimerisation domains-likeH: Viral glycoprotein, central and dimerisation domains (From Topology)T: Viral glycoprotein, central and dimerisation domainsF: Flavi_glycoprotECOD (1.6)
DFlavi_propepe6idkD1 A: beta sandwichesX: HSP40/DnaJ peptide-binding domain (From Topology)H: HSP40/DnaJ peptide-binding domain (From Topology)T: HSP40/DnaJ peptide-binding domainF: Flavi_propepECOD (1.6)
EFlavi_propepe6idkE1 A: beta sandwichesX: HSP40/DnaJ peptide-binding domain (From Topology)H: HSP40/DnaJ peptide-binding domain (From Topology)T: HSP40/DnaJ peptide-binding domainF: Flavi_propepECOD (1.6)
FFlavi_propepe6idkF1 A: beta sandwichesX: HSP40/DnaJ peptide-binding domain (From Topology)H: HSP40/DnaJ peptide-binding domain (From Topology)T: HSP40/DnaJ peptide-binding domainF: Flavi_propepECOD (1.6)
G [auth H]V-set_8e6idkH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
H [auth I]V-set_8e6idkI1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
K [auth M]V-set_8e6idkM1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
I [auth J]V-set_3e6idkJ1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
J [auth L]V-set_3e6idkL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
L [auth N]V-set_3e6idkN1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
G [auth H],
H [auth I],
K [auth M]
Fab 1H10 VH Homo sapiens (human) IGHV3-30*01, IGHV3-30*03, IGHV3-30*04, IGHV3-30*06, IGHV3-30*07, IGHV3-30*08, IGHV3-30*09, IGHV3-30*11, IGHV3-30*12, IGHV3-30*14, IGHV3-30*16, IGHV3-30*17, IGHV3-30*19, IGHV3-30-3*01, IGHV3-33*05, IGHV3-30-3*03, IGHJ6*01 V-DOMAIN VH IG VH-V-LAMBDA IMGT (202533-0)
I [auth J],
J [auth L],
L [auth N]
Fab 1H10 V-LAMBDA Homo sapiens (human) IGLV1-47*01, IGLJ2*01, IGLJ3*02, IGLJ3*01 V-DOMAIN V-LAMBDA IG VH-V-LAMBDA IMGT (202533-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
G [auth H],
H [auth I],
K [auth M]
Heavy ChainIGHV3 -premembrane proteinSAbDab (2025-08-29)
I [auth J],
J [auth L],
L [auth N]
Light ChainIGLV1 Lambdapremembrane proteinSAbDab (2025-08-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C
PF00869Flavivirus glycoprotein, central and dimerisation domains (Flavi_glycoprot)Flavivirus glycoprotein, central and dimerisation domainsDomain
A, B, C
PF21659Flavivirus envelope glycoprotein E, stem/anchor domain (Flavi_E_stem)Flavivirus envelope glycoprotein E, stem/anchor domainThis entry represents the stem/anchor domain found at the C-terminal of envelope glycoprotein E from Flavivirus. This domain comprises a stem region followed by two transmembrane anchor domains [1-5]. Domain
A, B, C
PF02832Flavivirus glycoprotein, immunoglobulin-like domain (Flavi_glycop_C)Flavivirus glycoprotein, immunoglobulin-like domainDomain
D, E, F
PF01570Flavivirus polyprotein propeptide (Flavi_propep)Flavivirus polyprotein propeptide- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C
Envelope protein
D, E, F
Premembrane protein
G [auth H],
H [auth I],
K [auth M]
Fab 1H10 heavy chain (V-region)---
I [auth J],
J [auth L],
L [auth N]
Fab 1H10 light chain (V-region)---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C
IPR000208RNA-directed RNA polymerase, fingers/palm subdomains, flavivirusDomain
A, B, C
IPR014756Immunoglobulin E-setHomologous Superfamily
A, B, C
IPR001122Capsid protein C, flavivirusDomain
A, B, C
IPR027287Glycoprotein E, immunoglobulin-like domain, flavivirusDomain
A, B, C
IPR014412Genome polyprotein, FlavivirusFamily
A, B, C
IPR036253Flavivirus glycoprotein, central and dimerisation domain superfamilyHomologous Superfamily
A, B, C
IPR011492Non-structural protein NS3-like, DEAD-box helicase, flavivirusDomain
A, B, C
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
A, B, C
IPR026490mRNA cap 0/1 methyltransferaseDomain
A, B, C
IPR009003Peptidase S1, PA clanHomologous Superfamily
A, B, C
IPR001650Helicase, C-terminal domain-likeDomain
A, B, C
IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
A, B, C
IPR013755Flaviviral glycoprotein E, central domain, subdomain 1Homologous Superfamily
A, B, C
IPR000752Flavivirus non-structural protein NS2ADomain
A, B, C
IPR047530RNA-dependent RNA polymerase, flavivirusDomain
A, B, C
IPR049486Flavivridae NS3 helicase, C-terminal helical domainDomain
A, B, C
IPR046811RNA-directed RNA polymerase, thumb subdomain, flavivirusDomain
A, B, C
IPR038055Flaviviral glycoprotein E, dimerisation domainHomologous Superfamily
A, B, C
IPR002877Ribosomal RNA methyltransferase, FtsJ domainDomain
A, B, C
IPR038302Envelope glycoprotein M superfamily, flavivirusHomologous Superfamily
A, B, C
IPR000069Envelope glycoprotein M, flavivirusDomain
A, B, C
IPR038345Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamilyHomologous Superfamily
A, B, C
IPR038688Flavivirus polyprotein propeptide superfamilyHomologous Superfamily
A, B, C
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
A, B, C
IPR026470Flavivirus envelope glycoprotein E, Stem/Anchor domainDomain
A, B, C
IPR011998Envelope glycoprotein E, central and dimerisation domain, flavivirusDomain
A, B, C
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
A, B, C
IPR037172Flavivirus capsid protein C superfamilyHomologous Superfamily
A, B, C
IPR000404Flavivirus non-structural protein NS4ADomain
A, B, C
IPR000487Non-structural protein NS2B, flavivirusDomain
A, B, C
IPR001528Flavivirus non-structural protein NS4BDomain
A, B, C
IPR001157Non-structural protein NS1, flavivirusDomain
A, B, C
IPR013756Flaviviral glycoprotein E, central domain, subdomain 2Homologous Superfamily
A, B, C
IPR001850Non-structural protein NS3, peptidase S7, flavivirusDomain
A, B, C
IPR000336Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamilyHomologous Superfamily
A, B, C
IPR002535Flavivirus polyprotein propeptideDomain
A, B, C
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
A, B, C
IPR007094RNA-directed RNA polymerase, catalytic domainDomain
D, E, F
IPR000208RNA-directed RNA polymerase, fingers/palm subdomains, flavivirusDomain
D, E, F
IPR014756Immunoglobulin E-setHomologous Superfamily
D, E, F
IPR001122Capsid protein C, flavivirusDomain
D, E, F
IPR027287Glycoprotein E, immunoglobulin-like domain, flavivirusDomain
D, E, F
IPR014412Genome polyprotein, FlavivirusFamily
D, E, F
IPR036253Flavivirus glycoprotein, central and dimerisation domain superfamilyHomologous Superfamily
D, E, F
IPR011492Non-structural protein NS3-like, DEAD-box helicase, flavivirusDomain
D, E, F
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
D, E, F
IPR026490mRNA cap 0/1 methyltransferaseDomain
D, E, F
IPR009003Peptidase S1, PA clanHomologous Superfamily
D, E, F
IPR001650Helicase, C-terminal domain-likeDomain
D, E, F
IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
D, E, F
IPR013755Flaviviral glycoprotein E, central domain, subdomain 1Homologous Superfamily
D, E, F
IPR000752Flavivirus non-structural protein NS2ADomain
D, E, F
IPR047530RNA-dependent RNA polymerase, flavivirusDomain
D, E, F
IPR049486Flavivridae NS3 helicase, C-terminal helical domainDomain
D, E, F
IPR046811RNA-directed RNA polymerase, thumb subdomain, flavivirusDomain
D, E, F
IPR038055Flaviviral glycoprotein E, dimerisation domainHomologous Superfamily
D, E, F
IPR002877Ribosomal RNA methyltransferase, FtsJ domainDomain
D, E, F
IPR038302Envelope glycoprotein M superfamily, flavivirusHomologous Superfamily
D, E, F
IPR000069Envelope glycoprotein M, flavivirusDomain
D, E, F
IPR038345Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamilyHomologous Superfamily
D, E, F
IPR038688Flavivirus polyprotein propeptide superfamilyHomologous Superfamily
D, E, F
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
D, E, F
IPR026470Flavivirus envelope glycoprotein E, Stem/Anchor domainDomain
D, E, F
IPR011998Envelope glycoprotein E, central and dimerisation domain, flavivirusDomain
D, E, F
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
D, E, F
IPR037172Flavivirus capsid protein C superfamilyHomologous Superfamily
D, E, F
IPR000404Flavivirus non-structural protein NS4ADomain
D, E, F
IPR000487Non-structural protein NS2B, flavivirusDomain
D, E, F
IPR001528Flavivirus non-structural protein NS4BDomain
D, E, F
IPR001157Non-structural protein NS1, flavivirusDomain
D, E, F
IPR013756Flaviviral glycoprotein E, central domain, subdomain 2Homologous Superfamily
D, E, F
IPR001850Non-structural protein NS3, peptidase S7, flavivirusDomain
D, E, F
IPR000336Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamilyHomologous Superfamily
D, E, F
IPR002535Flavivirus polyprotein propeptideDomain
D, E, F
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
D, E, F
IPR007094RNA-directed RNA polymerase, catalytic domainDomain