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- PDB-5y0a: Cryo-EM structure of zika virus complexed with Fab of ZKA190 at p... -

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Entry
Database: PDB / ID: 5y0a
TitleCryo-EM structure of zika virus complexed with Fab of ZKA190 at pH 8.0 and 37 celsius degree
Descriptorprotein E
variable region of Fab ZKA190 heavy chain
variable region of Fab ZKA190 light chain
KeywordsVIRUS/IMMUNE SYSTEM / virus / antibody / complex / VIRUS-IMMUNE SYSTEM complex / icosahedral virus
Specimen sourceZika virus (strain Mr 766) / virus / ZIKV
Homo sapiens / human
MethodElectron microscopy (22 Å resolution / Particle / Single particle)
AuthorsWang, J.Q. / Lok, S.M.
CitationCell, 2017, 171, 229-241.e15

primary. Cell, 2017, 171, 229-241.e15 Yorodumi Papers
A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential.
Jiaqi Wang / Marco Bardelli / Diego A Espinosa / Mattia Pedotti / Thiam-Seng Ng / Siro Bianchi / Luca Simonelli / Elisa X Y Lim / Mathilde Foglierini / Fabrizia Zatta / Stefano Jaconi / Martina Beltramello / Elisabetta Cameroni / Guntur Fibriansah / Jian Shi / Taylor Barca / Isabel Pagani / Alicia Rubio / Vania Broccoli / Elisa Vicenzi / Victoria Graham / Steven Pullan / Stuart Dowall / Roger Hewson / Simon Jurt / Oliver Zerbe / Karin Stettler / Antonio Lanzavecchia / Federica Sallusto / Andrea Cavalli / Eva Harris / Shee-Mei Lok / Luca Varani / Davide Corti

#1. To Be Published Search PubMed
Cryo-EM structure of zika virus complexed with a human monoclonal antibody
Wang, J.Q. / Lok, S.M.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 15, 2017 / Release: Oct 4, 2017

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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
  • EMDB-6793
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Assembly

Deposited unit
A: protein E
C: protein E
B: protein E
H: variable region of Fab ZKA190 heavy chain
L: variable region of Fab ZKA190 light chain
F: variable region of Fab ZKA190 heavy chain
G: variable region of Fab ZKA190 light chain
D: variable region of Fab ZKA190 heavy chain
E: variable region of Fab ZKA190 light chain


Theoretical massNumber of molelcules
Total (without water)211,2469
Polyers211,2469
Non-polymers00
Water0
#1
A: protein E
C: protein E
B: protein E
H: variable region of Fab ZKA190 heavy chain
L: variable region of Fab ZKA190 light chain
F: variable region of Fab ZKA190 heavy chain
G: variable region of Fab ZKA190 light chain
D: variable region of Fab ZKA190 heavy chain
E: variable region of Fab ZKA190 light chain
x 60


Theoretical massNumber of molelcules
Total (without water)12,674,733540
Polyers12,674,733540
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: protein E
C: protein E
B: protein E
H: variable region of Fab ZKA190 heavy chain
L: variable region of Fab ZKA190 light chain
F: variable region of Fab ZKA190 heavy chain
G: variable region of Fab ZKA190 light chain
D: variable region of Fab ZKA190 heavy chain
E: variable region of Fab ZKA190 light chain
x 5


  • icosahedral pentamer
  • 1.06 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)1,056,22845
Polyers1,056,22845
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: protein E
C: protein E
B: protein E
H: variable region of Fab ZKA190 heavy chain
L: variable region of Fab ZKA190 light chain
F: variable region of Fab ZKA190 heavy chain
G: variable region of Fab ZKA190 light chain
D: variable region of Fab ZKA190 heavy chain
E: variable region of Fab ZKA190 light chain
x 6


  • icosahedral 23 hexamer
  • 1.27 MDa, 54 polymers
Theoretical massNumber of molelcules
Total (without water)1,267,47354
Polyers1,267,47354
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

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Components

#1: Polypeptide(L)protein E / Coordinate model: Cα atoms only


Mass: 44069.930 Da / Num. of mol.: 3 / Source: (gene. exp.) Zika virus (strain Mr 766) / virus / References: UniProt: A0A1V0E2E9

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)variable region of Fab ZKA190 heavy chain / Coordinate model: Cα atoms only


Mass: 14410.010 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens / human
#3: Polypeptide(L)variable region of Fab ZKA190 light chain / Coordinate model: Cα atoms only


Mass: 11935.241 Da / Num. of mol.: 3 / Source: (gene. exp.) 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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1zika virus complexed with Fab of a human monoclonal antibody named ZKA190COMPLEX1, 2, 30MULTIPLE SOURCES
2zika virusCOMPLEX21MULTIPLE SOURCES
3Fab ZKA190COMPLEX31MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Zika virus / Strain: Mr 766
Buffer solutionpH: 8
Buffer component
IDConc.UnitsFormulaBuffer ID
1120nMNaCl1
212mMTris-HCl1
31mMEDTA1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationCryogen name: ETHANE

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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 FIELD / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategoryImage processing IDImaging ID
1RelionPARTICLE SELECTION1
2LeginonIMAGE ACQUISITION1
4Ctffind3CTF CORRECTION1
10RelionINITIAL EULER ASSIGNMENT1
11RelionFINAL EULER ASSIGNMENT1
13RelionRECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I
3D reconstructionResolution: 22 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6728 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT

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