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- PDB-5h30: Cryo-EM structure of zika virus complexed with Fab C10 at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 5h30
TitleCryo-EM structure of zika virus complexed with Fab C10 at pH 6.5
Components
  • IgG C10 heavy chain
  • IgG C10 light chain
  • structural protein EStructure
  • strutural protein M
KeywordsVIRUS/IMMUNE SYSTEM / Antibody / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of innate immune response / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...negative regulation of innate immune response / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / molecular adaptor activity / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / centrosome / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / GTP binding / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / 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 / helicase superfamily c-terminal domain / Immunoglobulin E-set / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / 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 speciesHomo sapiens (human)
Zika virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZhang, S. / Kostyuchenko, V. / Ng, T.-S. / Lok, S.-M.
Funding support Singapore, United States, 3items
OrganizationGrant numberCountry
Ministry of Education Tier 3 grantMOE2012-T3-1-008 Singapore
National Research Foundation Investigatorship awardNRFI2016-01 Singapore
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100625 and AI 107731 United States
CitationJournal: Nat Commun / Year: 2016
Title: Neutralization mechanism of a highly potent antibody against Zika virus.
Authors: Shuijun Zhang / Victor A Kostyuchenko / Thiam-Seng Ng / Xin-Ni Lim / Justin S G Ooi / Sebastian Lambert / Ter Yong Tan / Douglas G Widman / Jian Shi / Ralph S Baric / Shee-Mei Lok /
Abstract: The rapid spread of Zika virus (ZIKV), which causes microcephaly and Guillain-Barré syndrome, signals an urgency to identify therapeutics. Recent efforts to rescreen dengue virus human antibodies ...The rapid spread of Zika virus (ZIKV), which causes microcephaly and Guillain-Barré syndrome, signals an urgency to identify therapeutics. Recent efforts to rescreen dengue virus human antibodies for ZIKV cross-neutralization activity showed antibody C10 as one of the most potent. To investigate the ability of the antibody to block fusion, we determined the cryoEM structures of the C10-ZIKV complex at pH levels mimicking the extracellular (pH8.0), early (pH6.5) and late endosomal (pH5.0) environments. The 4.0 Å resolution pH8.0 complex structure shows that the antibody binds to E proteins residues at the intra-dimer interface, and the virus quaternary structure-dependent inter-dimer and inter-raft interfaces. At pH6.5, antibody C10 locks all virus surface E proteins, and at pH5.0, it locks the E protein raft structure, suggesting that it prevents the structural rearrangement of the E proteins during the fusion event-a vital step for infection. This suggests antibody C10 could be a good therapeutic candidate.
History
DepositionOct 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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Assembly

Deposited unit
A: structural protein E
C: structural protein E
D: strutural protein M
B: structural protein E
E: strutural protein M
F: strutural protein M
G: IgG C10 heavy chain
H: IgG C10 light chain
K: IgG C10 heavy chain
L: IgG C10 light chain
I: IgG C10 heavy chain
M: IgG C10 light chain


Theoretical massNumber of molelcules
Total (without water)266,17912
Polymers266,17912
Non-polymers00
Water0
1
A: structural protein E
C: structural protein E
D: strutural protein M
B: structural protein E
E: strutural protein M
F: strutural protein M
G: IgG C10 heavy chain
H: IgG C10 light chain
K: IgG C10 heavy chain
L: IgG C10 light chain
I: IgG C10 heavy chain
M: IgG C10 light chain
x 60


Theoretical massNumber of molelcules
Total (without water)15,970,744720
Polymers15,970,744720
Non-polymers00
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
A: structural protein E
C: structural protein E
D: strutural protein M
B: structural protein E
E: strutural protein M
F: strutural protein M
G: IgG C10 heavy chain
H: IgG C10 light chain
K: IgG C10 heavy chain
L: IgG C10 light chain
I: IgG C10 heavy chain
M: IgG C10 light chain
x 5


  • icosahedral pentamer
  • 1.33 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,330,89560
Polymers1,330,89560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: structural protein E
C: structural protein E
D: strutural protein M
B: structural protein E
E: strutural protein M
F: strutural protein M
G: IgG C10 heavy chain
H: IgG C10 light chain
K: IgG C10 heavy chain
L: IgG C10 light chain
I: IgG C10 heavy chain
M: IgG C10 light chain
x 6


  • icosahedral 23 hexamer
  • 1.6 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)1,597,07472
Polymers1,597,07472
Non-polymers00
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
6
A: structural protein E
C: structural protein E
D: strutural protein M
B: structural protein E
E: strutural protein M
F: strutural protein M
G: IgG C10 heavy chain
H: IgG C10 light chain
K: IgG C10 heavy chain
L: IgG C10 light chain
I: IgG C10 heavy chain
M: IgG C10 light chain
x 60


  • crystal asymmetric unit, crystal frame
  • 16 MDa, 720 polymers
Theoretical massNumber of molelcules
Total (without water)15,970,744720
Polymers15,970,744720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein structural protein E / Structure / Coordinate model: Cα atoms only


Mass: 54444.051 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Zika virus / Strain: Mr 766 / References: UniProt: A0A024B7W1
#2: Protein strutural protein M / Coordinate model: Cα atoms only


Mass: 8496.883 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Zika virus / Strain: Mr 766 / References: UniProt: A0A024B7W1
#3: Antibody IgG C10 heavy chain / Coordinate model: Cα atoms only


Mass: 14487.058 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Antibody IgG C10 light chain / Coordinate model: Cα atoms only


Mass: 11298.362 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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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

Component
IDNameTypeEntity IDParent-IDSource
1Zika virus complexed with C10 Fab at pH 6.5COMPLEXall0MULTIPLE SOURCES
2Zika virusCOMPLEX#1-#21NATURAL
3Fab C10COMPLEX#3-#41RECOMBINANT
Source (natural)Organism: Zika virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T / Plasmid: unknown
Buffer solutionpH: 6.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 43 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45867 / Symmetry type: POINT

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