[English] 日本語
Yorodumi
- EMDB-64735: Cryo-EM structure of RSV pre-F monomer in complex with CNR2056/CNR2047 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64735
TitleCryo-EM structure of RSV pre-F monomer in complex with CNR2056/CNR2047
Map data
Sample
  • Complex: RSV pre-F monomer in complex with CNR2056/CNR2047
    • Complex: RSV Pre-fusion Protein
      • Protein or peptide: RSV Pre-fusion Protein
    • Complex: Antibody CNR2056
      • Protein or peptide: CNR2056 heavy chain
      • Protein or peptide: CNR2056 light chain
    • Complex: Antibody CNR2047
      • Protein or peptide: CNR2047 heavy chain
      • Protein or peptide: CNR2047 light chain
KeywordsRSV / Fusion Protein / Antibody / VIRAL PROTEIN
Biological speciesRespiratory syncytial virus A2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.27 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 20, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64735.png

Downloads & links

-
Map

FileDownload / File: emd_64735.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.284
Minimum - Maximum-0.23444673 - 0.93586236
Average (Standard dev.)0.006629424 (±0.040719416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_64735_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64735_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RSV pre-F monomer in complex with CNR2056/CNR2047

EntireName: RSV pre-F monomer in complex with CNR2056/CNR2047
Components
  • Complex: RSV pre-F monomer in complex with CNR2056/CNR2047
    • Complex: RSV Pre-fusion Protein
      • Protein or peptide: RSV Pre-fusion Protein
    • Complex: Antibody CNR2056
      • Protein or peptide: CNR2056 heavy chain
      • Protein or peptide: CNR2056 light chain
    • Complex: Antibody CNR2047
      • Protein or peptide: CNR2047 heavy chain
      • Protein or peptide: CNR2047 light chain

-
Supramolecule #1: RSV pre-F monomer in complex with CNR2056/CNR2047

SupramoleculeName: RSV pre-F monomer in complex with CNR2056/CNR2047 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Respiratory syncytial virus A2

-
Supramolecule #2: RSV Pre-fusion Protein

SupramoleculeName: RSV Pre-fusion Protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Respiratory syncytial virus A2

-
Supramolecule #3: Antibody CNR2056

SupramoleculeName: Antibody CNR2056 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #4: Antibody CNR2047

SupramoleculeName: Antibody CNR2047 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: CNR2056 heavy chain

MacromoleculeName: CNR2056 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.949546 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG VVQPGTSLTL SCAASGFTFR TYAFHWVRQA PGKGLEWLAL VTYDGTTQYY ADSVKGRLTI YRDNSKNTLF LHLNSLRRD DTAIYFCARG GEGSFSWLGY LQYMDVWGQG TTVTVSS

-
Macromolecule #2: RSV Pre-fusion Protein

MacromoleculeName: RSV Pre-fusion Protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus A2
Molecular weightTheoretical: 61.626539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNA VTELQLLMQS TPATNNRARR ELPRFMNYTL NNAKKTNVTL SKKRKRRFLG FLLGVGSAIA SGVAVCKVLH L EGEVNKIK ...String:
MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNA VTELQLLMQS TPATNNRARR ELPRFMNYTL NNAKKTNVTL SKKRKRRFLG FLLGVGSAIA SGVAVCKVLH L EGEVNKIK SALLSTNKAV VSLSNGVSVL TFKVLDLKNY IDKQLLPILN KQSCSISNIE TVIEFQQKNN RLLEITREFS VN AGVTTPV STYMLTNSEL LSLINDMPIT NDQKKLMSNN VQIVRQQSYS IMCIIKEEVL AYVVQLPLYG VIDTPCWKLH TSP LCTTNT KEGSNICLTR TDRGWYCDNA GSVSFFPQAE TCKVQSNRVF CDTMNSLTLP SEVNLCNVDI FNPKYDCKIM TSKT DVSSS VITSLGAIVS CYGKTKCTAS NKNRGIIKTF SNGCDYVSNK GVDTVSVGNT LYYVNKQEGK SLYVKGEPII NFYDP LVFP SDEFDASISQ VNEKINQSLA FIRKSDELLS AIGGYIPEAP RDGQAYVRKD GEWVLLSTFL GHHHHHHHH

-
Macromolecule #3: CNR2056 light chain

MacromoleculeName: CNR2056 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.61957 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASV SGSPGQSITL SCTGTSSDIG DYDYVSWYQK YPDTAPKLVI YDVSERPSGV STRFSGSKSG NTASLTISGL QPEDEADYY CNSYSSTNTL KFGGGTKLTV L

-
Macromolecule #4: CNR2047 heavy chain

MacromoleculeName: CNR2047 heavy chain / type: protein_or_peptide / ID: 4 / 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

-
Macromolecule #5: CNR2047 light chain

MacromoleculeName: CNR2047 light chain / type: protein_or_peptide / ID: 5 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

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

4jhw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 62532
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more