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- PDB-5h37: Cryo-EM structure of zika virus complexed with Fab C10 at pH 8.0 -

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Entry
Database: PDB / ID: 5h37
TitleCryo-EM structure of zika virus complexed with Fab C10 at pH 8.0
Components
  • C10 IgG heavy chain variable region
  • C10 IgG light chain variable region
  • structural protein EStructure
  • strutural protein M
KeywordsVIRUS/IMMUNE SYSTEM / IgG NAG / VIRUS-IMMUNE SYSTEM complex
Function / homologyHelicase, C-terminal / Flavivirus capsid protein C / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Envelope glycoprotein M, flavivirus / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily ...Helicase, C-terminal / Flavivirus capsid protein C / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Envelope glycoprotein M, flavivirus / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS1 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS4B / Immunoglobulin E-set / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / DEAD box, Flavivirus / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Genome polyprotein, Flavivirus / Envelope glycoprotein M superfamily, flavivirus / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus NS2B domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Flavivirus DEAD domain / Flavivirus glycoprotein, immunoglobulin-like domain / FtsJ-like methyltransferase / Flavivirus polyprotein propeptide / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS2A / Flavivirus envelope glycoprotein M / Flavivirus capsid protein C / Flavivirus non-structural protein NS2B / Flavivirus RNA-directed RNA polymerase / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus non-structural Protein NS1 / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Helicase superfamily 1/2, ATP-binding domain / suppression by virus of host TYK2 activity / flavivirin / suppression by virus of host STAT2 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / suppression by virus of host STAT1 activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / ATP-dependent helicase activity / suppression by virus of host type I interferon-mediated signaling pathway / RNA helicase activity / 4 iron, 4 sulfur cluster binding / double-stranded RNA binding / RNA helicase / nucleoside-triphosphate phosphatase / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / clathrin-dependent endocytosis of virus by host cell / viral RNA genome replication / fusion of virus membrane with host endosome membrane / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / extracellular region / ATP binding / metal ion binding / Genome polyprotein
Function and homology information
Specimen sourceHomo sapiens (human)
Zika virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsZhang, S. / Kostyuchenko, V. / Ng, T.-S. / Lim, X.-N. / Ooi, J.S.G. / Lambert, S. / Tan, T.Y. / Widman, D. / Shi, J. / Baric, R.S. / Lok, S.-M.
Funding supportSingapore , United States , 3 items
OrganizationGrant numberCountry
Ministry of Education Tier 3 grantMOE2012-T3-1-008Singapore
National Research Foundation Investigatorship awardNRF-NRFI2016-01Singapore
NIH AIDAI100625 and AI 107731United 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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 20, 2016 / Release: Nov 30, 2016
RevisionDateData content typeGroupProviderType
1.0Nov 30, 2016Structure modelrepositoryInitial release
1.1Jan 25, 2017Structure modelDatabase references

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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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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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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: C10 IgG heavy chain variable region
H: C10 IgG light chain variable region
K: C10 IgG heavy chain variable region
L: C10 IgG light chain variable region
I: C10 IgG heavy chain variable region
M: C10 IgG light chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,40013
Polyers266,17912
Non-polymers2211
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: C10 IgG heavy chain variable region
H: C10 IgG light chain variable region
K: C10 IgG heavy chain variable region
L: C10 IgG light chain variable region
I: C10 IgG heavy chain variable region
M: C10 IgG light chain variable region
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)15,984,016780
Polyers15,970,744720
Non-polymers13,27260
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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: C10 IgG heavy chain variable region
H: C10 IgG light chain variable region
K: C10 IgG heavy chain variable region
L: C10 IgG light chain variable region
I: C10 IgG heavy chain variable region
M: C10 IgG light chain variable region
hetero molecules
x 5


  • icosahedral pentamer
  • 1.33 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,332,00165
Polyers1,330,89560
Non-polymers1,1065
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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: C10 IgG heavy chain variable region
H: C10 IgG light chain variable region
K: C10 IgG heavy chain variable region
L: C10 IgG light chain variable region
I: C10 IgG heavy chain variable region
M: C10 IgG light chain variable region
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.6 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)1,598,40278
Polyers1,597,07472
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
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: C10 IgG heavy chain variable region
H: C10 IgG light chain variable region
K: C10 IgG heavy chain variable region
L: C10 IgG light chain variable region
I: C10 IgG heavy chain variable region
M: C10 IgG light chain variable region
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 16 MDa, 720 polymers
Theoretical massNumber of molelcules
Total (without water)15,984,016780
Polyers15,970,744720
Non-polymers13,27260
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60

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Components

#1: Protein/peptide structural protein E / Structure


Mass: 54444.051 Da / Num. of mol.: 3 / Source: (natural) Zika virus / Strain: Mr 766 / References: UniProt: A0A024B7W1
#2: Protein/peptide strutural protein M


Mass: 8496.883 Da / Num. of mol.: 3 / Source: (natural) Zika virus / Strain: Mr 766 / References: UniProt: A0A024B7W1
#3: Protein/peptide C10 IgG heavy chain variable region


Mass: 14487.058 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Protein/peptide C10 IgG light chain variable region


Mass: 11298.362 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#5: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1zika virus complexed with C10 Fab at pH 8.0COMPLEX1, 2, 3, 4, 50MULTIPLE SOURCES
2zika virusCOMPLEX1, 21NATURAL
3C10 FabCOMPLEX3, 41RECOMBINANT
Source (natural)Organism: Zika virus
Source (recombinant)Cell: HEK293T / Organism: Homo sapiens (human) / Plasmid: unknown
Buffer solutionpH: 8
SpecimenEmbedding 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
MicroscopyMicroscope model: 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: 38 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 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 49100 / Symmetry type: POINT

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