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- EMDB-64670: Cryo-EM structure of RSV pre-F in complex with antibody CNR2047 -

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Basic information

Entry
Database: EMDB / ID: EMD-64670
TitleCryo-EM structure of RSV pre-F in complex with antibody CNR2047
Map data
Sample
  • Complex: RSV pre-F in complex with antibody CNR2047
    • Complex: RSV Pre-fusion Protein
      • Protein or peptide: RSV Pre-fusion Protein
    • 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: 3.78 Å
AuthorsZhai H / Deng J / Yu W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of RSV pre-F in complex with antibody CNR2047
Authors: Zhai H / Deng J / Yu W
History
DepositionMay 18, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64670.png

Downloads & links

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Map

FileDownload / File: emd_64670.map.gz / Format: CCP4 / Size: 64 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 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.257
Minimum - Maximum-0.88077706 - 1.3140848
Average (Standard dev.)0.0039478987 (±0.0384927)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_64670_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64670_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RSV pre-F in complex with antibody CNR2047

EntireName: RSV pre-F in complex with antibody CNR2047
Components
  • Complex: RSV pre-F in complex with antibody CNR2047
    • Complex: RSV Pre-fusion Protein
      • Protein or peptide: RSV Pre-fusion Protein
    • Complex: Antibody CNR2047
      • Protein or peptide: CNR2047 Heavy Chain
      • Protein or peptide: CNR2047 Light Chain

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Supramolecule #1: RSV pre-F in complex with antibody CNR2047

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

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Supramolecule #2: RSV Pre-fusion Protein

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

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Supramolecule #3: Antibody CNR2047

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

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Macromolecule #1: RSV Pre-fusion Protein

MacromoleculeName: RSV Pre-fusion Protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / 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

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Macromolecule #2: CNR2047 Heavy Chain

MacromoleculeName: CNR2047 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / 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 #3: CNR2047 Light Chain

MacromoleculeName: CNR2047 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / 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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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:

4jhw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 39908
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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