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- PDB-9bbn: Cryo-EM structure of Chikungunya virus asymmetric unit with Fab C9 -

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Basic information

Entry
Database: PDB / ID: 9bbn
TitleCryo-EM structure of Chikungunya virus asymmetric unit with Fab C9
Components
  • Capsid protein
  • E1 glycoprotein
  • E2 glycoprotein
  • E3 glycoprotein
  • Heavy chain of C9
  • Light chain of C9
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / CHIKV asymmetric unit with Fab C9 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


T=4 icosahedral viral capsid / 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 ...T=4 icosahedral viral capsid / 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 / 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 speciesMus musculus (house mouse)
Chikungunya virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSu, G.C. / Galaz-Montoya, J.G. / Pintilie, G. / Jin, J. / Chiu, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103832 United States
CitationJournal: To Be Published
Title: Cryogenic Electron Microscopy Reveals Dual-Inhibition Mechanisms and Explains the Differential Neutralization Potency of Two anti-CHIKV Antibodies
Authors: Su, G.C. / Galaz-Montoya, J.G. / Pintilie, G. / Jin, J. / Chiu, W.
History
DepositionApr 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
U: E3 glycoprotein
W: E3 glycoprotein
X: E3 glycoprotein
C: E1 glycoprotein
G: E2 glycoprotein
A: E1 glycoprotein
E: E2 glycoprotein
M: Heavy chain of C9
N: Light chain of C9
B: E1 glycoprotein
O: Heavy chain of C9
P: Light chain of C9
F: E2 glycoprotein
J: Capsid protein
K: Capsid protein
Q: Heavy chain of C9
R: Light chain of C9
I: Capsid protein
D: E1 glycoprotein
S: Heavy chain of C9
T: Light chain of C9
H: E2 glycoprotein
L: Capsid protein
V: E3 glycoprotein


Theoretical massNumber of molelcules
Total (without water)663,07424
Polymers663,07424
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 16 molecules UWXVCABDGEFHJKIL

#1: Protein
E3 glycoprotein


Mass: 6955.070 Da / Num. of mol.: 4 / Fragment: UNP residues 266-325 / Source method: isolated from a natural source / Source: (natural) Chikungunya virus / Strain: vaccine strain 181/clone / References: UniProt: D2KBQ2, togavirin
#2: Protein
E1 glycoprotein


Mass: 47497.906 Da / Num. of mol.: 4 / Fragment: UNP residues 810-1248 / Source method: isolated from a natural source / Source: (natural) Chikungunya virus / Strain: vaccine strain 181/clone / References: UniProt: Q88628, togavirin
#3: Protein
E2 glycoprotein


Mass: 47077.719 Da / Num. of mol.: 4 / Fragment: UNP residues 330-748 / Source method: isolated from a natural source / Source: (natural) Chikungunya virus / Strain: vaccine strain 181/clone 25 / References: UniProt: Q88628, togavirin
#6: Protein
Capsid protein


Mass: 16428.607 Da / Num. of mol.: 4 / Fragment: UNP residues 111-261 / Source method: isolated from a natural source / Source: (natural) Chikungunya virus / Strain: vaccine strain 181/clone 25 / References: UniProt: Q88628, togavirin

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Antibody , 2 types, 8 molecules MOQSNPRT

#4: Antibody
Heavy chain of C9


Mass: 24747.697 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#5: Antibody
Light chain of C9


Mass: 23061.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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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 virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Chikungunya virus / Strain: vaccine strain 181/clone 25
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 700 nm / Triangulation number (T number): 4
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
120 mMTris1
2120 mMSodium chloride1
31 mMEDTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 106000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7ISOLDEmodel fitting
8MDFFmodel fitting
10PHENIXmodel refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 192895
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1151475 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8FCG

8fcg


Accession code: 8FCG / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00247636
ELECTRON MICROSCOPYf_angle_d0.5864868
ELECTRON MICROSCOPYf_dihedral_angle_d11.6417304
ELECTRON MICROSCOPYf_chiral_restr0.0557288
ELECTRON MICROSCOPYf_plane_restr0.0048376

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