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- PDB-9v2r: Cryo-EM structure of RSV pre-F trimer in complex with CNR2056/CNR2047 -

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Basic information

Entry
Database: PDB / ID: 9v2r
TitleCryo-EM structure of RSV pre-F trimer in complex with CNR2056/CNR2047
Components
  • CNR2047 heavy chain
  • CNR2047 light chain
  • CNR2056 heavy chain
  • CNR2056 light chain
  • RSV Pre-fusion Protein
KeywordsVIRAL PROTEIN / RSV / Fusion Protein / Antibody
Biological speciesHomo sapiens (human)
Respiratory syncytial virus A2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZhai, H. / Deng, J. / Yu, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Transl Med / Year: 2026
Title: Antibody cocktails based on the occupationally acquired immunity of pediatricians neutralize and confer protection against RSV and hMPV.
Authors: Hui Zhai / Wenxiang Yu / Jinyue Wang / Jie Deng / Siyu Lei / Teng Zhou / Yixin Li / Kaijun Xu / Mengyang Ma / Rui Feng / Yaling Hu / Luo Ren / Yunlong Cao / Enmei Liu / Xiangxi Wang /
Abstract: Human respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are major causes of severe respiratory infections in young children, older adults, and immunocompromised individuals. Here, we ...Human respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are major causes of severe respiratory infections in young children, older adults, and immunocompromised individuals. Here, we isolated RSV fusion (F) protein-specific B cells from pediatricians who are routinely exposed to these viruses. We then derived monoclonal antibodies (mAbs) from those B cells to characterize their binding and neutralization profiles. Among the isolated mAbs, we found that CNR2056 and CNR2053 (targeting site Ø of the pre-F protein) potently neutralized diverse RSV A and B strains; another mAb, CNR2047 (targeting site III), uniquely exhibited cross-neutralization capacity against both RSV and hMPV variants. In vivo, prophylactic administration of CNR2056 and CNR2053 controlled lung viral loads and pathology in RSV A2- and B9320-challenged cotton rats. Moreover, a prophylactic dose of 0.5 milligrams per kilogram of CNR2047 resulted in complete protection against hMPV in the lungs of BALB/c mice. Structural analysis revealed unique binding modes for the three mAbs, supporting the potential for rational mAb cocktail design. Deep mutational scanning for RSV F further demonstrated that mutations required to evade CNR2053 and CNR2056 were primarily in evolutionarily constrained sites, suggesting a fitness cost to immune escape. Rationally combining site Ø- and site III-directed mAbs (e.g., CNR2056-CNR2047) into cocktails conferred additive effects, expanding coverage to hMPV and minimizing risk of escape variants. Thus, rationally designed cocktails of CNR2056, CNR2053, and CNR2047 may offer a versatile immunoprophylactic agent against a range of pneumoviruses with potential to protect against both current and future variants.
History
DepositionMay 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CNR2056 heavy chain
B: RSV Pre-fusion Protein
C: CNR2056 light chain
D: CNR2047 heavy chain
E: CNR2047 light chain
F: CNR2056 heavy chain
H: RSV Pre-fusion Protein
J: CNR2056 light chain
L: CNR2047 heavy chain
N: CNR2047 light chain
G: CNR2056 heavy chain
I: RSV Pre-fusion Protein
K: CNR2056 light chain
M: CNR2047 heavy chain
O: CNR2047 light chain


Theoretical massNumber of molelcules
Total (without water)335,58315
Polymers335,58315
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody CNR2056 heavy chain


Mass: 13949.546 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: 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)
#3: Antibody CNR2056 light chain


Mass: 11619.570 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody CNR2047 heavy chain


Mass: 12947.601 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody CNR2047 light chain


Mass: 11717.903 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 trimer in complex with CNR2056/CNR2047COMPLEXall0RECOMBINANT
2RSV Pre-fusion ProteinCOMPLEX#21RECOMBINANT
3Antibody CNR2056COMPLEX#1, #31RECOMBINANT
4Antibody CNR2047COMPLEX#4-#51RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Respiratory syncytial virus A21972429
32Respiratory syncytial virus A21972429
43Homo sapiens (human)9606
54Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Homo 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 TECNAI 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: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12437 / Symmetry type: POINT
RefinementHighest resolution: 4.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421459
ELECTRON MICROSCOPYf_angle_d0.9129118
ELECTRON MICROSCOPYf_dihedral_angle_d6.3022958
ELECTRON MICROSCOPYf_chiral_restr0.0543348
ELECTRON MICROSCOPYf_plane_restr0.0063699

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