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- EMDB-6466: Cryo-EM of CHIKV VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-6466
TitleCryo-EM of CHIKV VLP
Map dataReconstruction of CHIKV virus-like particle
Sample
  • Sample: Virus-like particle of Chikungunya virus (S27)
  • Virus: Chikungunya virus
Keywordschikungunya / cryo-EM
Biological speciesChikungunya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 15.3 Å
AuthorsJin J / Liss N / Chen D-H / Liao M / Fox JM / Shimak RM / Fong RH / Chafets D / Bakkour S / Keating S ...Jin J / Liss N / Chen D-H / Liao M / Fox JM / Shimak RM / Fong RH / Chafets D / Bakkour S / Keating S / Fomin ME / Muench MO / Sherman MB / Doranz BJ / Diamond MS / Simmons G
CitationJournal: Cell Rep / Year: 2015
Title: Neutralizing Monoclonal Antibodies Block Chikungunya Virus Entry and Release by Targeting an Epitope Critical to Viral Pathogenesis.
Authors: Jing Jin / Nathan M Liss / Dong-Hua Chen / Maofu Liao / Julie M Fox / Raeann M Shimak / Rachel H Fong / Daniel Chafets / Sonia Bakkour / Sheila Keating / Marina E Fomin / Marcus O Muench / ...Authors: Jing Jin / Nathan M Liss / Dong-Hua Chen / Maofu Liao / Julie M Fox / Raeann M Shimak / Rachel H Fong / Daniel Chafets / Sonia Bakkour / Sheila Keating / Marina E Fomin / Marcus O Muench / Michael B Sherman / Benjamin J Doranz / Michael S Diamond / Graham Simmons /
Abstract: We evaluated the mechanism by which neutralizing human monoclonal antibodies inhibit chikungunya virus (CHIKV) infection. Potently neutralizing antibodies (NAbs) blocked infection at multiple steps ...We evaluated the mechanism by which neutralizing human monoclonal antibodies inhibit chikungunya virus (CHIKV) infection. Potently neutralizing antibodies (NAbs) blocked infection at multiple steps of the virus life cycle, including entry and release. Cryo-electron microscopy structures of Fab fragments of two human NAbs and chikungunya virus-like particles showed a binding footprint that spanned independent domains on neighboring E2 subunits within one viral spike, suggesting a mechanism for inhibiting low-pH-dependent membrane fusion. Detailed epitope mapping identified amino acid E2-W64 as a critical interaction residue. An escape mutation (E2-W64G) at this residue rendered CHIKV attenuated in mice. Consistent with these data, CHIKV-E2-W64G failed to emerge in vivo under the selection pressure of one of the NAbs, IM-CKV063. As our study suggests that antibodies engaging the residue E2-W64 can potently inhibit CHIKV at multiple stages of infection, antibody-based therapies or immunogens that target this region might have protective value.
History
DepositionSep 13, 2015-
Header (metadata) releaseOct 14, 2015-
Map releaseJan 13, 2016-
UpdateJan 13, 2016-
Current statusJan 13, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6466.gif

Downloads & links

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Map

FileDownload / File: emd_6466.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of CHIKV virus-like particle
Voxel sizeX=Y=Z: 3.14 Å
Density
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.02787305 - 0.07516
Average (Standard dev.)0.00221255 (±0.01082234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 1130.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.143.143.14
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z1130.4001130.4001130.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-189
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0280.0750.002

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Supplemental data

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Sample components

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Entire : Virus-like particle of Chikungunya virus (S27)

EntireName: Virus-like particle of Chikungunya virus (S27)
Components
  • Sample: Virus-like particle of Chikungunya virus (S27)
  • Virus: Chikungunya virus

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Supramolecule #1000: Virus-like particle of Chikungunya virus (S27)

SupramoleculeName: Virus-like particle of Chikungunya virus (S27) / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Chikungunya virus

SupramoleculeName: Chikungunya virus / type: virus / ID: 1 / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Sci species strain: S27 / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 680 Å / T number (triangulation number): 4

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4 / Details: 20 mM HEPES, 150 mM NaCl
GridDetails: Quantifoil copper grids (R2/1, 200 mesh)
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 2.5 seconds before plunging.

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification.
DateSep 25, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Digitization - Sampling interval: 15.6 µm / Number real images: 350 / Average electron dose: 18 e/Å2 / Bits/pixel: 32
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.3 Å / Resolution method: OTHER / Software - Name: Relion_1.3 / Number images used: 5510
DetailsParticle images were automatically boxed out using the program ethan.

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Atomic model buiding 1

Initial modelPDB ID:

3j2w


Chain - #0 - Chain ID: B / Chain - #1 - Chain ID: C / Chain - #2 - Chain ID: D / Chain - #3 - Chain ID: N / Chain - #4 - Chain ID: O / Chain - #5 - Chain ID: P
SoftwareName: Chimera
DetailsThe fitting was done manually first, then with "Fit in Map" in Chimera.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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