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- PDB-5any: Electron cryo-microscopy of chikungunya virus in complex with neu... -

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Basic information

Entry
Database: PDB / ID: 5any
TitleElectron cryo-microscopy of chikungunya virus in complex with neutralizing antibody Fab CHK265
Components
  • E1
  • E2
  • FAB CHK265
  • FABFragment antigen-binding
KeywordsVIRUS / CHIKUNGUNYA VIRUS / NEUTRALIZING ANTIBODY FAB
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis ...T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesCHIKUNGUNYA VIRUS
MUS MUSCULUS (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16.9 Å
AuthorsFox, J.M. / Long, F. / Edeling, M.A. / Lin, H. / Duijl-Richter, M. / Fong, R.H. / Kahle, K.M. / Smit, J.M. / Jin, J. / Simmons, G. ...Fox, J.M. / Long, F. / Edeling, M.A. / Lin, H. / Duijl-Richter, M. / Fong, R.H. / Kahle, K.M. / Smit, J.M. / Jin, J. / Simmons, G. / Doranz, B.J. / Crowe, J.E. / Fremont, D.H. / Rossmann, M.G. / Diamond, M.S.
CitationJournal: Cell / Year: 2015
Title: Broadly Neutralizing Alphavirus Antibodies Bind an Epitope on E2 and Inhibit Entry and Egress.
Authors: Julie M Fox / Feng Long / Melissa A Edeling / Hueylie Lin / Mareike K S van Duijl-Richter / Rachel H Fong / Kristen M Kahle / Jolanda M Smit / Jing Jin / Graham Simmons / Benjamin J Doranz / ...Authors: Julie M Fox / Feng Long / Melissa A Edeling / Hueylie Lin / Mareike K S van Duijl-Richter / Rachel H Fong / Kristen M Kahle / Jolanda M Smit / Jing Jin / Graham Simmons / Benjamin J Doranz / James E Crowe / Daved H Fremont / Michael G Rossmann / Michael S Diamond /
Abstract: We screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of ...We screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of broadly neutralizing MAbs protected mice against infection by chikungunya, Mayaro, and O'nyong'nyong alphaviruses. Using alanine-scanning mutagenesis, loss-of-function recombinant proteins and viruses, and multiple functional assays, we determined that broadly neutralizing MAbs block multiple steps in the viral lifecycle, including entry and egress, and bind to a conserved epitope on the B domain of the E2 glycoprotein. A 16 Å resolution cryo-electron microscopy structure of a Fab fragment bound to CHIKV E2 B domain provided an explanation for its neutralizing activity. Binding to the B domain was associated with repositioning of the A domain of E2 that enabled cross-linking of neighboring spikes. Our results suggest that B domain antigenic determinants could be targeted for vaccine or antibody therapeutic development against multiple alphaviruses of global concern.
History
DepositionSep 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Oct 3, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-3144
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  • Superimposition on EM map
  • EMDB-3144
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E1
B: E2
C: E1
D: E2
E: E1
F: E2
G: E1
H: E2
I: FAB CHK265
J: FAB CHK265
K: FAB CHK265
L: FAB CHK265
M: FAB
N: FAB
O: FAB
P: FAB


Theoretical massNumber of molelcules
Total (without water)542,42116
Polymers542,42116
Non-polymers00
Water0
1
A: E1
B: E2
C: E1
D: E2
E: E1
F: E2
G: E1
H: E2
I: FAB CHK265
J: FAB CHK265
K: FAB CHK265
L: FAB CHK265
M: FAB
N: FAB
O: FAB
P: FAB
x 60


Theoretical massNumber of molelcules
Total (without water)32,545,252960
Polymers32,545,252960
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: E1
B: E2
C: E1
D: E2
E: E1
F: E2
G: E1
H: E2
I: FAB CHK265
J: FAB CHK265
K: FAB CHK265
L: FAB CHK265
M: FAB
N: FAB
O: FAB
P: FAB
x 5


  • icosahedral pentamer
  • 2.71 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)2,712,10480
Polymers2,712,10480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: E1
B: E2
C: E1
D: E2
E: E1
F: E2
G: E1
H: E2
I: FAB CHK265
J: FAB CHK265
K: FAB CHK265
L: FAB CHK265
M: FAB
N: FAB
O: FAB
P: FAB
x 6


  • icosahedral 23 hexamer
  • 3.25 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)3,254,52596
Polymers3,254,52596
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
E1


Mass: 48776.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHIKUNGUNYA VIRUS / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q1H8W5
#2: Protein
E2


Mass: 39907.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHIKUNGUNYA VIRUS / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q1H8W5
#3: Antibody
FAB CHK265


Mass: 23743.719 Da / Num. of mol.: 4 / Fragment: HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#4: Antibody
FAB / Fragment antigen-binding


Mass: 23177.713 Da / Num. of mol.: 4 / Fragment: LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)

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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

ComponentName: chikungunya virus in complex with neutralizing antibody Fab CHK265Chikungunya
Type: COMPLEX
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Mar 10, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 47000 X / Calibrated magnification: 78354 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 22 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 500

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Processing

EM softwareName: jspr / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 16.9 Å / Num. of particles: 5828
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3144. (DEPOSITION ID: 13751)
Symmetry type: POINT
RefinementHighest resolution: 16.9 Å
Refinement stepCycle: LAST / Highest resolution: 16.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35620 0 0 0 35620

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