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- EMDB-9131: Cryo-EM structure of the ZIKV virion in complex with Fab fragment... -

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Entry
Database: EMDB / ID: EMD-9131
TitleCryo-EM structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195
Map data
SampleZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195:
virus / monoclonal antibody ZIKV-195 / E protein / M protein / (monoclonal antibody ZIKV-195 ...) x 2 / ligand
Function / homology
Function and homology information


immunoglobulin production / suppression by virus of host TYK2 activity / immunoglobulin complex / flavivirin / methyltransferase cap1 / suppression by virus of host STAT2 activity / mRNA (guanine-N7)-methyltransferase / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host STAT1 activity / mRNA (guanine-N7-)-methyltransferase activity ...immunoglobulin production / suppression by virus of host TYK2 activity / immunoglobulin complex / flavivirin / methyltransferase cap1 / suppression by virus of host STAT2 activity / mRNA (guanine-N7)-methyltransferase / 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 / suppression by virus of host type I interferon-mediated signaling pathway / double-stranded RNA binding / RNA helicase / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / viral capsid / induction by virus of host autophagy / RNA-directed RNA polymerase / clathrin-dependent endocytosis of virus by host cell / viral RNA genome replication / RNA helicase activity / adaptive immune response / fusion of virus membrane with host endosome membrane / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / immune response / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / serine-type endopeptidase activity / structural molecule activity / extracellular space / integral component of membrane / extracellular region / ATP binding / plasma membrane / metal ion binding
Peptidase S1, PA clan / Immunoglobulin-like fold / Flavivirus non-structural protein NS4B / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS1 / Flavivirus capsid protein C / DEAD box, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flaviviral glycoprotein E, central domain, subdomain 2 ...Peptidase S1, PA clan / Immunoglobulin-like fold / Flavivirus non-structural protein NS4B / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS1 / Flavivirus capsid protein C / DEAD box, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flaviviral glycoprotein E, central domain, subdomain 2 / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2B / Flaviviral glycoprotein E, central domain, subdomain 1 / Immunoglobulin V-set domain / Flavivirus non-structural protein NS4A / Flavivirus glycoprotein central and dimerisation domain / Envelope glycoprotein M, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / P-loop containing nucleoside triphosphate hydrolase / Immunoglobulin-like domain / RNA-directed RNA polymerase, catalytic domain / Ribosomal RNA methyltransferase FtsJ domain / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus polyprotein propeptide / Envelope glycoprotein M superfamily, flavivirus / Flaviviral glycoprotein E, dimerisation domain / Flavivirus NS3, petidase S7 / Helicase, C-terminal / Flavivirus capsid protein C superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / RNA-directed RNA polymerase, flavivirus
Genome polyprotein / Immunoglobulin lambda variable 1-36
Biological speciesZika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) / Homo sapiens (human) / ZIKV (virus) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsLong F / Rossmann MG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)AI076331 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structural basis of a potent human monoclonal antibody against Zika virus targeting a quaternary epitope.
Authors: Feng Long / Michael Doyle / Estefania Fernandez / Andrew S Miller / Thomas Klose / Madhumati Sevvana / Aubrey Bryan / Edgar Davidson / Benjamin J Doranz / Richard J Kuhn / Michael S Diamond ...Authors: Feng Long / Michael Doyle / Estefania Fernandez / Andrew S Miller / Thomas Klose / Madhumati Sevvana / Aubrey Bryan / Edgar Davidson / Benjamin J Doranz / Richard J Kuhn / Michael S Diamond / James E Crowe / Michael G Rossmann /
Abstract: Zika virus (ZIKV) is a major human pathogen and member of the genus in the Flaviviridae family. In contrast to most other insect-transmitted flaviviruses, ZIKV also can be transmitted sexually and ...Zika virus (ZIKV) is a major human pathogen and member of the genus in the Flaviviridae family. In contrast to most other insect-transmitted flaviviruses, ZIKV also can be transmitted sexually and from mother to fetus in humans. During recent outbreaks, ZIKV infections have been linked to microcephaly, congenital disease, and Guillain-Barré syndrome. Neutralizing antibodies have potential as therapeutic agents. We report here a 4-Å-resolution cryo-electron microscopy structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195. The footprint of the ZIKV-195 Fab fragment expands across two adjacent envelope (E) protein protomers. ZIKV neutralization by this antibody is presumably accomplished by cross-linking the E proteins, which likely prevents formation of E protein trimers required for fusion of the viral and cellular membranes. A single dose of ZIKV-195 administered 5 days after virus inoculation showed marked protection against lethality in a stringent mouse model of infection.
Validation ReportPDB-ID: 6mid

SummaryFull reportAbout validation report
History
DepositionSep 19, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseJan 16, 2019-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 15
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6mid
  • Surface level: 15
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6mid
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9131.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 512 pix.
= 829.44 Å
1.62 Å/pix.
x 512 pix.
= 829.44 Å
1.62 Å/pix.
x 512 pix.
= 829.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Density
Contour LevelBy AUTHOR: 15 / Movie #1: 15
Minimum - Maximum-101.69505 - 169.9646
Average (Standard dev.)0.16021295 (±7.2527075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 829.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.621.621.62
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z829.440829.440829.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-101.695169.9650.160

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Supplemental data

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Half map: Half map #1

Fileemd_9131_half_map_1.map
AnnotationHalf map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map #2

Fileemd_9131_half_map_2.map
AnnotationHalf map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire ZIKV virion in complex with Fab fragments of the potently neutral...

EntireName: ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195
Details: Purified from infected Vero cells overexpressing the furin protease
Number of components: 8

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Component #1: protein, ZIKV virion in complex with Fab fragments of the potentl...

ProteinName: ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195
Details: Purified from infected Vero cells overexpressing the furin protease
Recombinant expression: No

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Component #2: virus, Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)

VirusName: Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013

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Component #3: protein, monoclonal antibody ZIKV-195

ProteinName: monoclonal antibody ZIKV-195 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #4: protein, E protein

ProteinName: E protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 54.444051 kDa
SourceSpecies: ZIKV (virus) / Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013

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Component #5: protein, M protein

ProteinName: M protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 8.496883 kDa
SourceSpecies: ZIKV (virus) / Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013

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Component #6: protein, monoclonal antibody ZIKV-195 heavy chain

ProteinName: monoclonal antibody ZIKV-195 heavy chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.148739 kDa
SourceSpecies: Human (human)

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Component #7: protein, monoclonal antibody ZIKV-195 light chain

ProteinName: monoclonal antibody ZIKV-195 light chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.750902 kDa
SourceSpecies: Human (human)

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Component #8: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / Buffer solution: NTE buffer at pH 8.0 / pH: 8
Support filmunspecified
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1691

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 10687
3D reconstructionSoftware: jspr / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The map was masked by removing the internal nucleic acid region and the external background region.
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Details: The occupancy of bound Fabs was low. Due to poor density, only the variable domain of Fab molecule was modeled and fit into one of the three Fab binding sites on each icosahedral asymmetric unit.
Input PDB model: 6CO8
Output model

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