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- PDB-3j2w: Electron cryo-microscopy of Chikungunya virus -

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Basic information

Entry
Database: PDB / ID: 3j2w
TitleElectron cryo-microscopy of Chikungunya virus
Components
  • (Glycoprotein ...) x 5
  • Capsid protein
KeywordsVIRUS / E1-E2 glycoprotein / nucleocapsid protein / transmembrane helix
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / identical protein binding / membrane
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 / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 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 1.1Jun 8, 2016Group: Structure summary
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list / struct_ref_seq_dif
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_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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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
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-5577
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoprotein E1
M: Glycoprotein E2
B: Glycoprotein E1
N: Glycoprotein E2
C: Glycoprotein E1
O: Glycoprotein E2
D: Glycoprotein E1
P: Glycoprotein E2
E: Glycoprotein E1
Q: Glycoprotein E2
F: Glycoprotein E1
R: Glycoprotein E2
G: Glycoprotein E1
S: Glycoprotein E2
H: Glycoprotein E1
T: Glycoprotein E2
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein


Theoretical massNumber of molelcules
Total (without water)441,69320
Polymers441,69320
Non-polymers00
Water00
1
A: Glycoprotein E1
M: Glycoprotein E2
B: Glycoprotein E1
N: Glycoprotein E2
C: Glycoprotein E1
O: Glycoprotein E2
D: Glycoprotein E1
P: Glycoprotein E2
E: Glycoprotein E1
Q: Glycoprotein E2
F: Glycoprotein E1
R: Glycoprotein E2
G: Glycoprotein E1
S: Glycoprotein E2
H: Glycoprotein E1
T: Glycoprotein E2
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)26,501,6061200
Polymers26,501,6061200
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: Glycoprotein E1
M: Glycoprotein E2
B: Glycoprotein E1
N: Glycoprotein E2
C: Glycoprotein E1
O: Glycoprotein E2
D: Glycoprotein E1
P: Glycoprotein E2
E: Glycoprotein E1
Q: Glycoprotein E2
F: Glycoprotein E1
R: Glycoprotein E2
G: Glycoprotein E1
S: Glycoprotein E2
H: Glycoprotein E1
T: Glycoprotein E2
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
x 5


  • icosahedral pentamer
  • 2.21 MDa, 100 polymers
Theoretical massNumber of molelcules
Total (without water)2,208,467100
Polymers2,208,467100
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Glycoprotein E1
M: Glycoprotein E2
B: Glycoprotein E1
N: Glycoprotein E2
C: Glycoprotein E1
O: Glycoprotein E2
D: Glycoprotein E1
P: Glycoprotein E2
E: Glycoprotein E1
Q: Glycoprotein E2
F: Glycoprotein E1
R: Glycoprotein E2
G: Glycoprotein E1
S: Glycoprotein E2
H: Glycoprotein E1
T: Glycoprotein E2
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 2.65 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,650,161120
Polymers2,650,161120
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

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Glycoprotein ... , 5 types, 16 molecules ABCDMNOPEFGHQRST

#1: Protein
Glycoprotein E1


Mass: 42712.309 Da / Num. of mol.: 4 / Fragment: UNP residues 810-1202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 37997 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q1H8W5
#2: Protein Glycoprotein E2


Mass: 37848.852 Da / Num. of mol.: 3 / Fragment: UNP residues 332-667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 37997 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q1H8W5
#3: Protein Glycoprotein E2


Mass: 37866.891 Da / Num. of mol.: 1 / Fragment: UNP residues 332-667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 37997 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q1H8W5
#4: Protein/peptide
Glycoprotein E1


Mass: 4810.723 Da / Num. of mol.: 4 / Fragment: UNP residues 668-748
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 37997 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3
#5: Protein
Glycoprotein E2


Mass: 8817.458 Da / Num. of mol.: 4 / Fragment: UNP residues 1203-1248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 37997 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3

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Protein , 1 types, 4 molecules IJKL

#6: Protein
Capsid protein


Mass: 16229.508 Da / Num. of mol.: 4 / Fragment: UNP residues 113-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 37997 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3

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Details

Has protein modificationY

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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 VLP / Type: VIRUS
Details of virusEmpty: NO / Enveloped: YES / Host category: INVERTEBRATES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Aedes albopictus
Buffer solutionName: PBS / pH: 7 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh copper grid (1.2 um hole)
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 100 K / Humidity: 100 %
Details: Blot for 2 seconds before plunging into liquid ethane (FEI VITROBOT MARK I)
Method: Blot for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jan 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Cs: 2.7 mm
Astigmatism: Objective lens astigmatism was corrected at 250000 times magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GENERIC FILM
Image scansNum. digital images: 1532
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2EMAN3D reconstruction
3FREALIGN3D reconstruction
CTF correctionDetails: each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 36236 / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Details: REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 3N43

3n43


Accession code: 3N43 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms30928 0 0 0 30928

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