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- PDB-4uok: Electron Cryo-microscopy of Venezuelan Equine Encephalitis Virus ... -

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Entry
Database: PDB / ID: 4uok
TitleElectron Cryo-microscopy of Venezuelan Equine Encephalitis Virus TC-83 in complex with neutralizing antibody Fab 3B4C-4
Components
  • FAB FRAGMENT HEAVY CHAINFragment antigen-binding
  • FAB FRAGMENT LIGHT CHAINFragment antigen-binding
KeywordsIMMUNE SYSTEM / VIRAL PROTEIN / ALPHAVIRUS / VENEZUELAN / ANTIBODY NEUTRALIZATION / FAB
Specimen sourceHOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 18 Å resolution
AuthorsPorta, J. / Jose, J. / Roehrig, J.T. / Blair, C.D. / Kuhn, R.J. / G Rossmann, M.
CitationJournal: J. Virol. / Year: 2014
Title: Locking and blocking the viral landscape of an alphavirus with neutralizing antibodies.
Authors: Jason Porta / Joyce Jose / John T Roehrig / Carol D Blair / Richard J Kuhn / Michael G Rossmann
Abstract: Alphaviruses are serious, sometimes lethal human pathogens that belong to the family Togaviridae. The structures of human Venezuelan equine encephalitis virus (VEEV), an alphavirus, in complex with ...Alphaviruses are serious, sometimes lethal human pathogens that belong to the family Togaviridae. The structures of human Venezuelan equine encephalitis virus (VEEV), an alphavirus, in complex with two strongly neutralizing antibody Fab fragments (F5 and 3B4C-4) have been determined using a combination of cryo-electron microscopy and homology modeling. We characterize these monoclonal antibody Fab fragments, which are known to abrogate VEEV infectivity by binding to the E2 (envelope) surface glycoprotein. Both of these antibody Fab fragments cross-link the surface E2 glycoproteins and therefore probably inhibit infectivity by blocking the conformational changes that are required for making the virus fusogenic. The F5 Fab fragment cross-links E2 proteins within one trimeric spike, whereas the 3B4C-4 Fab fragment cross-links E2 proteins from neighboring spikes. Furthermore, F5 probably blocks the receptor-binding site, whereas 3B4C-4 sterically hinders the exposure of the fusion loop at the end of the E2 B-domain.
IMPORTANCE: Alphaviral infections are transmitted mainly by mosquitoes. Venezuelan equine encephalitis virus (VEEV) is an alphavirus with a wide distribution across the globe. No effective vaccines exist for alphaviral infections. Therefore, a better understanding of VEEV and its associated neutralizing antibodies will help with the development of effective drugs and vaccines.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 4, 2014 / Release: Sep 17, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 17, 2014Structure modelrepositoryInitial release
1.1Oct 1, 2014Structure modelOther / Source and taxonomy / Structure summary
1.2Aug 23, 2017Structure modelData collectionem_software_em_software.image_processing_id

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Assembly

Deposited unit
A: FAB FRAGMENT HEAVY CHAIN
L: FAB FRAGMENT LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)47,0572
Polyers47,0572
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein/peptide FAB FRAGMENT HEAVY CHAIN / Fragment antigen-binding


Mass: 23406.305 Da / Num. of mol.: 1 / Source: (gene. exp.) HOMO SAPIENS (human)
Description: HUMANIZED FABS USING COMBINATORIAL ANTIBODY LIBRARIES AND PHAGE DISPLAY TECHNOLOGY
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10F
#2: Protein/peptide FAB FRAGMENT LIGHT CHAIN / Fragment antigen-binding


Mass: 23650.797 Da / Num. of mol.: 1 / Source: (gene. exp.) HOMO SAPIENS (human)
Description: HUMANIZED FABS USING COMBINATORIAL ANTIBODY LIBRARIES AND PHAGE DISPLAY TECHNOLOGY
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10F

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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

ComponentName: VENEZUELAN EQUINE ENCEPHALITIS VIRUS STRAIN TC-83 / Type: VIRUS
Buffer solutionName: 0.5 M NACL, 10 MM TRIS PH 7.6, 5 MM EDTA / Details: 0.5 M NACL, 10 MM TRIS PH 7.6, 5 MM EDTA / pH: 7.6
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Oct 14, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Calibrated magnification: 60521 / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 kelvins
Image recordingElectron dose: 24 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 104

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Processing

EM software
IDNameVersionCategory
1EMAN13D reconstruction
2EMAN23D reconstruction
CTF correctionDetails: EACH IMAGE
SymmetryPoint symmetry: I
3D reconstructionMethod: COMMON LINES / Resolution: 18 Å / Number of particles: 1120 / Nominal pixel size: 1.07 / Actual pixel size: 1.11
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2655. (DEPOSITION ID: 12522).
Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--HOMOLOGY / Ref protocol: OTHER / Ref space: REAL
Least-squares processHighest resolution: 18 Å
Refine hist #LASTHighest resolution: 18 Å
Number of atoms included #LASTProtein: 3308 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3308

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