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- EMDB-64671: Cryo-EM structure of hMPV pre-F in complex with antibody CNR2047 -

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Basic information

Entry
Database: EMDB / ID: EMD-64671
TitleCryo-EM structure of hMPV pre-F in complex with antibody CNR2047
Map data
Sample
  • Complex: hMPV antibody CNR2047
    • Complex: hMPV Fusion Protein
      • Protein or peptide: hMPV fusion protein
    • Complex: CNR2047
      • Protein or peptide: CNR2047 heavy chain
      • Protein or peptide: CNR2047 light chain
KeywordshMPV / Fusion Protein / Antibody / VIRAL PROTEIN
Biological speciesHuman metapneumovirus A / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.12 Å
AuthorsZhai H / Deng J / Yu W
Funding support1 items
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 18, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64671.png

Downloads & links

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Map

FileDownload / File: emd_64671.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 220 pix.
= 227.92 Å		1.04 Å/pix.
x 220 pix.
= 227.92 Å		1.04 Å/pix.
x 220 pix.
= 227.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.036 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.332
Minimum - Maximum-0.75787354 - 1.4037699
Average (Standard dev.)0.001397231 (±0.0390629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 227.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64671_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_64671_half_map_2.map
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Sample components

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Entire : hMPV antibody CNR2047

EntireName: hMPV antibody CNR2047
Components
  • Complex: hMPV antibody CNR2047
    • Complex: hMPV Fusion Protein
      • Protein or peptide: hMPV fusion protein
    • Complex: CNR2047
      • Protein or peptide: CNR2047 heavy chain
      • Protein or peptide: CNR2047 light chain

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Supramolecule #1: hMPV antibody CNR2047

SupramoleculeName: hMPV antibody CNR2047 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human metapneumovirus A

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Supramolecule #2: hMPV Fusion Protein

SupramoleculeName: hMPV Fusion Protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Human metapneumovirus A

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Supramolecule #3: CNR2047

SupramoleculeName: CNR2047 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CNR2047 heavy chain

MacromoleculeName: CNR2047 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.947601 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVESGGGL VKPGESLRLS CAVSGSMFSS YVMHWVRQAP GKGLDWVSSI TGGGNYISYA DSVKGRFIIS RDNGRNSLSL QMSSLRVDD TAVYYCVRGL SGVMGVTWFD SWGQGTLVTV SS

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Macromolecule #2: CNR2047 light chain

MacromoleculeName: CNR2047 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.717903 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGFDVHWYQH LPGKAPKVII YENSHRPSGV PDRFFGSKSG TSASLSISGL QPEDEADYY CQSYDRGLDW VFGGGTKLTV L

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Macromolecule #3: hMPV fusion protein

MacromoleculeName: hMPV fusion protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human metapneumovirus A
Molecular weightTheoretical: 59.332301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSWKVVIIFS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC ADGPSLIKTE LDLTKSALRE LRTVSADQL AREEQIENPR RRRFVLGAIA LGVATAAAVT AGVAIAKTIR LESEVTAIKN ALKKTNEAVS TLGNGVRVLA T AVRELKDF ...String:
MSWKVVIIFS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC ADGPSLIKTE LDLTKSALRE LRTVSADQL AREEQIENPR RRRFVLGAIA LGVATAAAVT AGVAIAKTIR LESEVTAIKN ALKKTNEAVS TLGNGVRVLA T AVRELKDF VSKNLTRAIN KNKCDIPDLK MAVSFSQFNR RFLNVVRQFS DNAGITPAIS LDLMTDAELA RAVSNMPTSA GQ IKLMLEN RAMVRRKGFG ILIGVYGSSV IYMVQLPIFG VIDTPCWIVK AAPSCSEKKG NYACLLREDQ GWYCQNAGST VYY PNEKDC ETRGDHVFCD TAAGINVAEQ SKECNINIST TNYPCKVSTG RHPISMVALS PLGALVACYK GVSCSIGSNR VGII KQLNK GCSYITNQDA DTVTIDNTVY QLSKVEGEQH VIKGRPVSSS FDPVKFPEDQ FNVALDQVFE SIENSQALVD QSNRI LSSA EKGNTSGREN LYFQGGGGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGGIE GRHHHHHH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5wb0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 49711
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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