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- PDB-9v0n: Cryo-EM structure of RSV pre-F in complex with antibody CNR2042 -

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Basic information

Entry
Database: PDB / ID: 9v0n
TitleCryo-EM structure of RSV pre-F in complex with antibody CNR2042
Components
  • CNR2042 Heavy Chain
  • CNR2042 Light Chain
  • RSV Pre-fusion Protein
KeywordsVIRAL PROTEIN / RSV / Fusion Protein / Antibody
Biological speciesRespiratory syncytial virus A2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsZhai, H. / Deng, J. / Yu, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of RSV pre-F in complex with antibody CNR2042
Authors: Zhai, H. / Deng, J. / Yu, W.
History
DepositionMay 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 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

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Assembly

Deposited unit
A: RSV Pre-fusion Protein
C: CNR2042 Heavy Chain
B: CNR2042 Light Chain
D: RSV Pre-fusion Protein
H: CNR2042 Heavy Chain
F: CNR2042 Light Chain
E: RSV Pre-fusion Protein
I: CNR2042 Heavy Chain
G: CNR2042 Light Chain


Theoretical massNumber of molelcules
Total (without water)260,2909
Polymers260,2909
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

#1: Protein RSV Pre-fusion Protein


Mass: 61626.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus A2 / Production host: Homo sapiens (human)
#2: Antibody CNR2042 Heavy Chain


Mass: 13505.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody CNR2042 Light Chain


Mass: 11630.824 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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

Component
IDNameTypeEntity IDParent-IDSource
1RSV pre-F in complex with antibody CNR2042COMPLEXall0RECOMBINANT
2RSV Pre-fusion ProteinCOMPLEX#11RECOMBINANT
3Antibody CNR2042COMPLEX#2-#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Respiratory syncytial virus A21972429
22Respiratory syncytial virus A21972429
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42798 / Symmetry type: POINT
RefinementHighest resolution: 3.75 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315492
ELECTRON MICROSCOPYf_angle_d0.63421018
ELECTRON MICROSCOPYf_dihedral_angle_d4.5662121
ELECTRON MICROSCOPYf_chiral_restr0.0432445
ELECTRON MICROSCOPYf_plane_restr0.0042673

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