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- PDB-5gzr: Zika virus E protein complexed with a neutralizing antibody Z23-Fab -

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Basic information

Entry
Database: PDB / ID: 5gzr
TitleZika virus E protein complexed with a neutralizing antibody Z23-Fab
Components
  • Z23 Fab heavy chain
  • Z23 Fab light chain
  • structural protein EStructure
  • strutural protein M
KeywordsVIRUS / Zika virus / Neutralizing antibody / Single Particle Reconstruction
Function / homologyFlavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / 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 / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain ...Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / 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 / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Envelope glycoprotein M, flavivirus / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / Flavivirus non-structural protein NS1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Helicase, C-terminal / 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 superfamily / Flaviviral glycoprotein E, dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flavivirus non-structural protein NS4A / 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 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 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus glycoprotein central and dimerisation 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 innate immune response / host cell endoplasmic reticulum / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host STAT1 activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / ATP-dependent helicase activity / host cell membrane / suppression by virus of host type I interferon-mediated signaling pathway / RNA helicase activity / RNA helicase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / 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 / Genome polyprotein
Function and homology information
Specimen sourceHomo sapiens (human)
Zika virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9.4 Å resolution
AuthorsGao, G.G. / Shi, Y. / Peng, R. / Liu, S.
CitationJournal: Sci Transl Med / Year: 2016
Title: Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus.
Authors: Qihui Wang / Huabing Yang / Xiaoqing Liu / Lianpan Dai / Tong Ma / Jianxun Qi / Gary Wong / Ruchao Peng / Sheng Liu / Junfu Li / Shihua Li / Jian Song / Jianying Liu / Jianhua He / Hui Yuan / Ying Xiong / Yong Liao / Jianhua Li / Jianping Yang / Zhou Tong / Bryan D Griffin / Yuhai Bi / Mifang Liang / Xiaoning Xu / Chuan Qin / Gong Cheng / Xinzheng Zhang / Peiyi Wang / Xiangguo Qiu / Gary Kobinger / Yi Shi / Jinghua Yan / George F Gao
Abstract: The 2015-2016 outbreak of Zika virus (ZIKV) disease has affected many countries and is a major public health concern. ZIKV is associated with fetal microcephaly and neurological complications, and ...The 2015-2016 outbreak of Zika virus (ZIKV) disease has affected many countries and is a major public health concern. ZIKV is associated with fetal microcephaly and neurological complications, and countermeasures are needed to treat and prevent ZIKV infection. We report the isolation of 13 specific human monoclonal antibodies from a single patient infected with ZIKV. Two of the isolated antibodies (Z23 and Z3L1) demonstrated potent ZIKV-specific neutralization in vitro without binding or neutralizing activity against strains 1 to 4 of dengue virus, the closest relative to ZIKV. These two antibodies provided postexposure protection to mice in vivo. Structural studies revealed that Z23 and Z3L1 bound to tertiary epitopes in envelope protein domain I, II, or III, indicating potential targets for ZIKV-specific therapy. Our results suggest the potential of antibody-based therapeutics and provide a structure-based rationale for the design of future ZIKV-specific vaccines.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 1, 2016 / Release: Nov 30, 2016
RevisionDateData content typeGroupProviderType
1.0Nov 30, 2016Structure modelrepositoryInitial release
1.1Dec 28, 2016Structure modelDatabase references

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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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Assembly

Deposited unit
A: structural protein E
B: structural protein E
C: structural protein E
D: strutural protein M
E: strutural protein M
F: strutural protein M
H: Z23 Fab heavy chain
L: Z23 Fab light chain
M: Z23 Fab heavy chain
N: Z23 Fab light chain


Theoretical massNumber of molelcules
Total (without water)282,69010
Polyers282,69010
Non-polymers00
Water0
1
A: structural protein E
B: structural protein E
C: structural protein E
D: strutural protein M
E: strutural protein M
F: strutural protein M
H: Z23 Fab heavy chain
L: Z23 Fab light chain
M: Z23 Fab heavy chain
N: Z23 Fab light chain
x 60


Theoretical massNumber of molelcules
Total (without water)16,961,372600
Polyers16,961,372600
Non-polymers00
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
B: structural protein E
C: structural protein E
D: strutural protein M
E: strutural protein M
F: strutural protein M
H: Z23 Fab heavy chain
L: Z23 Fab light chain
M: Z23 Fab heavy chain
N: Z23 Fab light chain
x 5


  • icosahedral pentamer
  • 1.41 MDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)1,413,44850
Polyers1,413,44850
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: structural protein E
B: structural protein E
C: structural protein E
D: strutural protein M
E: strutural protein M
F: strutural protein M
H: Z23 Fab heavy chain
L: Z23 Fab light chain
M: Z23 Fab heavy chain
N: Z23 Fab light chain
x 6


  • icosahedral 23 hexamer
  • 1.7 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,696,13760
Polyers1,696,13760
Non-polymers00
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
B: structural protein E
C: structural protein E
D: strutural protein M
E: strutural protein M
F: strutural protein M
H: Z23 Fab heavy chain
L: Z23 Fab light chain
M: Z23 Fab heavy chain
N: Z23 Fab light chain
x 60


  • crystal asymmetric unit, crystal frame
  • 17 MDa, 600 polymers
Theoretical massNumber of molelcules
Total (without water)16,961,372600
Polyers16,961,372600
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60

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Components

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


Mass: 54444.051 Da / Num. of mol.: 3 / Source: (natural) Zika virus / Cell line: Aedes albopictus C6/36 cells / Strain: isolate ZIKV_SMGC-1 / References: UniProt: A0A024B7W1, UniProt: A0A1B0XTC8*PLUS
#2: Protein/peptide strutural protein M / Coordinate model: Cα atoms only


Mass: 8496.883 Da / Num. of mol.: 3 / Source: (natural) Zika virus / Cell line: Aedes albopictus C6/36 cells / Strain: ZIKV_SMGC-1 / References: UniProt: A0A024B7W1, UniProt: A0A1B0XTC8*PLUS
#3: Protein/peptide Z23 Fab heavy chain / IgG heavy chain / Coordinate model: Cα atoms only


Mass: 23516.398 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Plasmid name: pCAGGS / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Protein/peptide Z23 Fab light chain / IgG light chain / Coordinate model: Cα atoms only


Mass: 23416.967 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Plasmid name: pCAGGS / 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 / Reconstruction method: single particle reconstruction

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Sample preparation

Component

Type: COMPLEX

IDNameEntity IDParent IDSourceDetails
1Zika virus in complex with a neutralizing antibody Z23 Fab1, 2, 3, 40MULTIPLE SOURCES
2Zika virus1, 21NATURALZika virus strain ZIKA-SMGC-1 propagated in Aedes albopictus C6/36 cells
3Neutralizing antibody Z23 Fab3, 41RECOMBINANT
Molecular weight
IDUnitsEntity assembly IDExperimental value
1MEGADALTONS1NO
21NO
31NO
Source (natural)Organism: Zika virus / Strain: ZIKA-SMGC-1
Source (recombinant)Cell: HEK293T / Organism: Homo sapiens (human) / Plasmid: pCAGGS
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
112 mMTris-HClTris-HCl1
2120 mMSodium ChlorideNaCl1
31 mMEthylenediaminetetraacetic acidEDTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 230 / Grid type: Zhongjikeyi ultra-thin carbon-coated copper grid
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins
Details: 3 uL Zika virus-Z23 Fab complex sample was transferred onto a glow-discharged ultra-thin carbon-coated copper grid (Purchased from Zhongjingkeyi Company, China) followed by 60s waiting and blotted for 2s with filter paper before plugging into liquid ethane using the FEI Vitrobot Mark IV

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 41139 / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Number of grids imaged: 1 / Number of real images: 566

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2.0particle selectione2boxer.py
4CTFFIND3.0CTF correction
7Chimera1.11model fitting
9Relion1.4initial Euler assignment
10Relion1.4final Euler assignment
11Relion1.4classification
12Relion1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 17024
SymmetryPoint symmetry: I
3D reconstructionResolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 3369 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT

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