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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: 9131
TitleCryo-EM structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195
Map dataZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195. Different contour levels are required to visualize the viral components and the bound Fab molecules.
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 / homologyHelicase, C-terminal / Flavivirus non-structural protein NS2A / Immunoglobulin-like domain superfamily / 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, C-terminal / Flavivirus non-structural protein NS2A / Immunoglobulin-like domain superfamily / 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 / 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 capsid protein C / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS1 / Flavivirus non-structural protein NS4B / Helicase superfamily 1/2, ATP-binding domain / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Immunoglobulin-like domain / Peptidase S1, PA clan / DEAD box, Flavivirus / Flavivirus glycoprotein central and dimerisation domain / Immunoglobulin V-set domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, central domain, subdomain 2 / Immunoglobulin-like fold / Flavivirus polyprotein propeptide / 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. / Ig-like domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Immunoglobulin V-set domain / Flavivirus DEAD domain / Flavivirus glycoprotein, immunoglobulin-like domain / FtsJ-like methyltransferase / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS4B / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, dimerisation domain / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus polyprotein propeptide superfamily / Flavivirus non-structural Protein NS1 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus RNA-directed RNA polymerase / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus envelope glycoprotein M / Flavivirus non-structural protein NS2A / immunoglobulin production / 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 / antigen binding / RNA helicase activity / 4 iron, 4 sulfur cluster binding / double-stranded RNA binding / RNA helicase / nucleoside-triphosphate phosphatase / viral capsid / adaptive immune response / 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 / immune response / protein dimerization activity / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / serine-type endopeptidase activity / extracellular space / integral component of membrane / extracellular region / ATP binding / plasma membrane
Function and homology information
SourceZika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) / Homo sapiens (human) / ZIKV (virus) / Human (human)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsLong F / Rossmann MG
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 / James E Crowe / Michael G Rossmann
Validation ReportPDB-ID: 6mid

SummaryFull reportAbout validation report
DateDeposition: Sep 19, 2018 / Header (metadata) release: Oct 3, 2018 / Map release: Jan 16, 2019 / Last update: Feb 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
  • 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
  • Download
  • 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

Fileemd_9131.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.62 Å/pix.
= 829.44 Å
512 pix
1.62 Å/pix.
= 829.44 Å
512 pix
1.62 Å/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 Level:15.0 (by author), 15 (movie #1):
Minimum - Maximum-101.695049999999995 - 169.96459999999999
Average (Standard dev.)0.16021295 (7.2527075)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin0.00.00.0
Limit511.0511.0511.0
Spacing512512512
CellA=B=C: 829.44 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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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: 3 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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