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

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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 / 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
Specimen sourceZika virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsLong, F. / Rossmann, M.G.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Sep 19, 2018 / Release: Jan 16, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 16, 2019Structure modelrepositoryInitial release
1.1Jan 30, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Feb 13, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Movie
  • 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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  • Superimposition on EM map
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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
Polyers214,7228
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
Polyers12,883,347480
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
Polyers1,073,61240
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
Polyers1,288,33548
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

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Components

#1: Protein/peptide E protein


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


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


Mass: 14148.739 Da / Num. of mol.: 1 / Fragment: Fab variable domain / Source: (natural) Homo sapiens (human)
#4: Protein/peptide monoclonal antibody ZIKV-195 light chain


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


Mass: 221.208 Da / Num. of mol.: 6 / 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
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 IDNcbi tax IDOrganismStrain
122043570Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)isolate ZIKV/Human/French Polynesia/10087PF/2013
239606Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionDetails: NTE buffer at pH 8.0 / pH: 8
Buffer component
IDConc.NameFormulaBuffer ID
120 mMTris1
2120 mMsodium chlorideNaCl1
31 mMEDTA1
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 kelvins

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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: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number 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
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number 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 buildingDetails: 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.
Ref protocol: FLEXIBLE FIT / Ref space: REAL
Atomic model buildingPDB-ID: 6CO8

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