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- PDB-3j2x: Electron Cryo-microscopy of Chikungunya VLP in complex with neutr... -

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Basic information

Entry
Database: PDB / ID: 3j2x
TitleElectron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab m242
Components
  • m242 heavy chain
  • m242 light chain
KeywordsIMMUNE SYSTEM / Alpha virus / Chikungunya VLP / neutralizing antibody m242
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15.6 Å
AuthorsSun, S. / Xiang, Y. / Rossmann, M.G.
CitationJournal: Elife / Year: 2013
Title: Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization.
Authors: Siyang Sun / Ye Xiang / Wataru Akahata / Heather Holdaway / Pankaj Pal / Xinzheng Zhang / Michael S Diamond / Gary J Nabel / Michael G Rossmann /
Abstract: A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 ...A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 glycoprotein heterodimer. The heterodimer structure was divided into domains to obtain a good fit to the cryoEM density. Differences in the T = 4 quasi-equivalent heterodimer components show their adaptation to different environments. The spikes on the icosahedral 3-fold axes and those in general positions are significantly different, possibly representing different phases during initial generation of fusogenic E1 trimers. CryoEM maps of neutralizing Fab fragments complexed with VLPs have been interpreted using the crystal structures of the Fab fragments and the VLP structure. Based on these analyses the CHK-152 antibody was shown to stabilize the viral surface, hindering the exposure of the fusion-loop, likely neutralizing infection by blocking fusion. The CHK-9, m10 and m242 antibodies surround the receptor-attachment site, probably inhibiting infection by blocking cell attachment. DOI:http://dx.doi.org/10.7554/eLife.00435.001.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_database_related / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_database_related.content_type / _pdbx_database_related.details / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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
  • EMDB-5576
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  • Superimposition on EM map
  • EMDB-5576
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: m242 light chain
B: m242 heavy chain
C: m242 light chain
D: m242 heavy chain
E: m242 light chain
F: m242 heavy chain
G: m242 light chain
H: m242 heavy chain


Theoretical massNumber of molelcules
Total (without water)188,2058
Polymers188,2058
Non-polymers00
Water0
1
A: m242 light chain
B: m242 heavy chain
C: m242 light chain
D: m242 heavy chain
E: m242 light chain
F: m242 heavy chain
G: m242 light chain
H: m242 heavy chain
x 60


Theoretical massNumber of molelcules
Total (without water)11,292,285480
Polymers11,292,285480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: m242 light chain
B: m242 heavy chain
C: m242 light chain
D: m242 heavy chain
E: m242 light chain
F: m242 heavy chain
G: m242 light chain
H: m242 heavy chain
x 5


  • icosahedral pentamer
  • 941 kDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)941,02440
Polymers941,02440
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: m242 light chain
B: m242 heavy chain
C: m242 light chain
D: m242 heavy chain
E: m242 light chain
F: m242 heavy chain
G: m242 light chain
H: m242 heavy chain
x 6


  • icosahedral 23 hexamer
  • 1.13 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)1,129,22948
Polymers1,129,22948
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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: Antibody
m242 light chain


Mass: 23854.242 Da / Num. of mol.: 4 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody
m242 heavy chain


Mass: 23196.947 Da / Num. of mol.: 4 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) 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

Component
IDNameTypeParent-ID
1Electron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab m242COMPLEX0
2m242 antibody Fab fragment1
3Chikungunya virus like particleVIRUS1
Details of virusEmpty: NO / Enveloped: YES / Host category: INVERTEBRATES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Aedes albopictus
Buffer solutionName: PBS / pH: 7.4 / Details: PBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh C-flat grids
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temp: 90 K / Humidity: 95 %
Details: Blot for 2 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3)
Method: Blot for 2 seconds before plunging

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/HE / Date: Jan 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 X / Calibrated magnification: 39190 X / Cs: 2 mm
Astigmatism: Objective lens astigmatism was corrected at 150000 times magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder
Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2
Image scansNum. digital images: 62
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1EMfitmodel fitting
2EMAN23D reconstruction
CTF correctionDetails: Each Micrograph
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 15.6 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1728 / Actual pixel size: 2.22 Å
Details: (Single particle details: The particles were selected using e2boxer) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Sumf / Details: REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 4GQ8

4gq8
PDB Unreleased entry


Pdb chain-ID: B / Accession code: 4GQ8 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms13228 0 0 0 13228

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