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- PDB-9vwm: Cryo-EM structure of zika virus complexed with Fab 1C11 -

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Basic information

Entry
Database: PDB / ID: 9vwm
TitleCryo-EM structure of zika virus complexed with Fab 1C11
Components
  • 1C11 Fab heavy chain variable region
  • 1C11 Fab light chain variable region
  • Envelope protein E
  • Small envelope protein M
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Virus / Antibody / Complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell nucleolus / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 5'-3' RNA polymerase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / 4 iron, 4 sulfur cluster binding / nucleoside-triphosphate phosphatase ...host cell nucleolus / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 5'-3' RNA polymerase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / 4 iron, 4 sulfur cluster binding / nucleoside-triphosphate phosphatase / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell cytoplasm / serine-type endopeptidase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / lipid binding / fusion of virus membrane with host endosome membrane / centrosome / viral envelope / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / metal ion binding / extracellular region / ATP binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Immunoglobulin E-set / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesMacaca mulatta (Rhesus monkey)
Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDai, L.P. / Lu, Y.M. / Yang, C.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of Zika virus in complex with Fab 1C11 at 3.21 Angstroms resolution.
Authors: Dai, L.P. / Lu, Y.M. / Yang, C.X.
History
DepositionJul 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Envelope protein E
C: Envelope protein E
F: Small envelope protein M
D: Small envelope protein M
K: 1C11 Fab heavy chain variable region
L: 1C11 Fab light chain variable region
I: 1C11 Fab heavy chain variable region
J: 1C11 Fab light chain variable region
A: Envelope protein E
B: Small envelope protein M
G: 1C11 Fab heavy chain variable region
H: 1C11 Fab light chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,86815
Polymers419,67012
Non-polymers2,1983
Water00
1
E: Envelope protein E
C: Envelope protein E
F: Small envelope protein M
D: Small envelope protein M
K: 1C11 Fab heavy chain variable region
L: 1C11 Fab light chain variable region
I: 1C11 Fab heavy chain variable region
J: 1C11 Fab light chain variable region
A: Envelope protein E
B: Small envelope protein M
G: 1C11 Fab heavy chain variable region
H: 1C11 Fab light chain variable region
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)25,312,054900
Polymers25,180,171720
Non-polymers131,883180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Envelope protein E
C: Envelope protein E
F: Small envelope protein M
D: Small envelope protein M
K: 1C11 Fab heavy chain variable region
L: 1C11 Fab light chain variable region
I: 1C11 Fab heavy chain variable region
J: 1C11 Fab light chain variable region
A: Envelope protein E
B: Small envelope protein M
G: 1C11 Fab heavy chain variable region
H: 1C11 Fab light chain variable region
hetero molecules
x 5


  • icosahedral pentamer
  • 2.11 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,109,33875
Polymers2,098,34860
Non-polymers10,99015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
E: Envelope protein E
C: Envelope protein E
F: Small envelope protein M
D: Small envelope protein M
K: 1C11 Fab heavy chain variable region
L: 1C11 Fab light chain variable region
I: 1C11 Fab heavy chain variable region
J: 1C11 Fab light chain variable region
A: Envelope protein E
B: Small envelope protein M
G: 1C11 Fab heavy chain variable region
H: 1C11 Fab light chain variable region
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 2.53 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,531,20590
Polymers2,518,01772
Non-polymers13,18818
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Envelope protein E


Mass: 54285.895 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
References: UniProt: A0A024B7W1
#2: Protein Small envelope protein M / Matrix protein


Mass: 8496.883 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
References: UniProt: A0A024B7W1
#3: Antibody 1C11 Fab heavy chain variable region


Mass: 52169.520 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#4: Antibody 1C11 Fab light chain variable region


Mass: 24937.543 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of Zika virus with Fab 1C11 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/20132043570ZIKV SMGC-1 strain
31Macaca mulatta (Rhesus monkey)9544
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8 / Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50154 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00219038
ELECTRON MICROSCOPYf_angle_d0.52425827
ELECTRON MICROSCOPYf_dihedral_angle_d6.7452835
ELECTRON MICROSCOPYf_chiral_restr0.0412928
ELECTRON MICROSCOPYf_plane_restr0.0033267

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