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- PDB-6mid: Cryo-EM structure of the ZIKV virion in complex with Fab fragment... -

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Basic information

Entry
Database: PDB / ID: 6mid
TitleCryo-EM structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195
Components
  • E protein
  • M protein
  • monoclonal antibody ZIKV-195 heavy chain
  • monoclonal antibody ZIKV-195 light chain
KeywordsVIRUS/IMMUNE SYSTEM / virus / monoclonal antibody / complex / VIRUS-IMMUNE SYSTEM complex
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
Flavivirus NS3, petidase S7 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Immunoglobulin-like fold / Flaviviral glycoprotein E, central domain, subdomain 2 / Flaviviral glycoprotein E, central domain, subdomain 1 / Immunoglobulin V-set domain ...Flavivirus NS3, petidase S7 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Immunoglobulin-like fold / Flaviviral glycoprotein E, central domain, subdomain 2 / Flaviviral glycoprotein E, central domain, subdomain 1 / Immunoglobulin V-set domain / Flavivirus glycoprotein central and dimerisation domain / DEAD box, Flavivirus / RNA-directed RNA polymerase, flavivirus / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / Flavivirus non-structural protein NS1 / Flavivirus non-structural protein NS4B / Helicase, C-terminal / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / mRNA cap 0/1 methyltransferase / P-loop containing nucleoside triphosphate hydrolase / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus capsid protein C superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin-like domain / S-adenosyl-L-methionine-dependent methyltransferase / Immunoglobulin-like domain superfamily / Monooxygenase - #260 / Flavivirus envelope glycoprotein M-like / Viral Envelope Glycoprotein, domain 2 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein; domain 3 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Monooxygenase / Helicase, Ruva Protein; domain 3 / Immunoglobulin-like / Up-down Bundle / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Genome polyprotein / Immunoglobulin lambda variable 1-36
Biological speciesZika virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsLong, F. / Rossmann, M.G.
Funding support United States, 1items
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 Report
SummaryFull reportAbout validation report
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
H: monoclonal antibody ZIKV-195 heavy chain
L: monoclonal antibody ZIKV-195 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,05014
Polymers214,7228
Non-polymers1,3276
Water0
1
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
H: monoclonal antibody ZIKV-195 heavy chain
L: monoclonal antibody ZIKV-195 light chain
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)12,962,981840
Polymers12,883,347480
Non-polymers79,635360
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
H: monoclonal antibody ZIKV-195 heavy chain
L: monoclonal antibody ZIKV-195 light chain
hetero molecules
x 5


  • icosahedral pentamer
  • 1.08 MDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)1,080,24870
Polymers1,073,61240
Non-polymers6,63630
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
H: monoclonal antibody ZIKV-195 heavy chain
L: monoclonal antibody ZIKV-195 light chain
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.3 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)1,296,29884
Polymers1,288,33548
Non-polymers7,96336
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein E protein


Mass: 54444.051 Da / Num. of mol.: 3 / Fragment: UNP residues 291-794 / Source method: isolated from a natural source
Source: (natural) Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013 / References: UniProt: A0A024B7W1
#2: Protein M protein


Mass: 8496.883 Da / Num. of mol.: 3 / Fragment: UNP residues 216-290 / Source method: isolated from a natural source
Source: (natural) Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013 / References: UniProt: A0A024B7W1
#3: Antibody monoclonal antibody ZIKV-195 heavy chain


Mass: 14148.739 Da / Num. of mol.: 1 / Fragment: Fab variable domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: Antibody monoclonal antibody ZIKV-195 light chain


Mass: 11750.902 Da / Num. of mol.: 1 / Fragment: Fab variable domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A0B4J1U3
#5: Sugar
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6

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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
IDNameTypeDetailsEntity IDParent-IDSource
1ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195COMPLEXPurified from infected Vero cells overexpressing the furin protease1, 2, 3, 40MULTIPLE SOURCES
2Zika virusVIRUS1, 21NATURAL
3monoclonal antibody ZIKV-195COMPLEX3, 41NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)2043570isolate ZIKV/Human/French Polynesia/10087PF/2013
23Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8 / Details: NTE buffer at pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2120 mMsodium chlorideNaClSodium chloride1
31 mMEDTAEthylenediaminetetraacetic acid1
SpecimenConc.: 1 mg/ml
Details: Fab fragments were mixed with purified mature virus particles to make complexes.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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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: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1691

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Processing

EM software
IDNameVersionCategoryDetails
1FindEMparticle selection
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
8EMfitmodel fitting
10jsprinitial Euler assignment
11jsprfinal Euler assignment
12RELIONclassification
13jspr3D reconstruction
20PHENIXmodel refinementreal space refinement
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10687
Details: The map was masked by removing the internal nucleic acid region and the external background region.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / 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.
Atomic model buildingPDB-ID: 6CO8

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