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- EMDB-63208: Cryo-EM structure of RSV pre-F (sc9-10 DS-Cav1, strain A2) in com... -

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Basic information

Entry
Database: EMDB / ID: EMD-63208
TitleCryo-EM structure of RSV pre-F (sc9-10 DS-Cav1, strain A2) in complex with Fabs 1A2 and 1B6
Map data
Sample
  • Complex: RSV pre-F protein in complex with Fabs 1A2 and 1B6
    • Complex: RSV pre-F protein
      • Protein or peptide: RSV pre-F protein
    • Complex: 1B6 Fab
      • Protein or peptide: 1B6 heavy chain
      • Protein or peptide: 1B6 light chain
    • Complex: 1A2 Fab
      • Protein or peptide: 1A2 heavy chain
      • Protein or peptide: 1A2 light chain
KeywordsRSV / Fusion protein / Antibody / Complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesRespiratory syncytial virus A2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLiu L / Zheng Q / Li S / Zheng Z / Xia N
Funding support China, 1 items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: Cryo-EM structure of RSV pre-F (sc9-10 DS-Cav1, strain A2) in complex with Fabs 1A2 and 1B6
Authors: Liu L / Zheng Q / Li S
History
DepositionJan 17, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63208.png

Downloads & links

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Map

FileDownload / File: emd_63208.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 450 pix.
= 292.5 Å		0.65 Å/pix.
x 450 pix.
= 292.5 Å		0.65 Å/pix.
x 450 pix.
= 292.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.046022702 - 1.9151899
Average (Standard dev.)0.0020107797 (±0.029633509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 292.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63208_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63208_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 protein in complex with Fabs 1A2 and 1B6

EntireName: RSV pre-F protein in complex with Fabs 1A2 and 1B6
Components
  • Complex: RSV pre-F protein in complex with Fabs 1A2 and 1B6
    • Complex: RSV pre-F protein
      • Protein or peptide: RSV pre-F protein
    • Complex: 1B6 Fab
      • Protein or peptide: 1B6 heavy chain
      • Protein or peptide: 1B6 light chain
    • Complex: 1A2 Fab
      • Protein or peptide: 1A2 heavy chain
      • Protein or peptide: 1A2 light chain

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Supramolecule #1: RSV pre-F protein in complex with Fabs 1A2 and 1B6

SupramoleculeName: RSV pre-F protein in complex with Fabs 1A2 and 1B6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Respiratory syncytial virus A2

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Supramolecule #2: RSV pre-F protein

SupramoleculeName: RSV pre-F protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Respiratory syncytial virus A2

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Supramolecule #3: 1B6 Fab

SupramoleculeName: 1B6 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2, #4

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Supramolecule #4: 1A2 Fab

SupramoleculeName: 1A2 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3, #5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RSV pre-F protein

MacromoleculeName: RSV pre-F protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus A2
Molecular weightTheoretical: 58.381605 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLGALRT GWYTSVITIE LSNIKEIKCN GTDAKVKLIK QELDKYKNA VTDLQLLMQS TPATGSGSAI CSGVAVCKVL HLEGEVNKIK SALLSTNKAV VSLSNGVSVL TFKVLDLKNY I DKQLLPIL ...String:
MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLGALRT GWYTSVITIE LSNIKEIKCN GTDAKVKLIK QELDKYKNA VTDLQLLMQS TPATGSGSAI CSGVAVCKVL HLEGEVNKIK SALLSTNKAV VSLSNGVSVL TFKVLDLKNY I DKQLLPIL NKQSCSIPNI ETVIEFQQKN NRLLEITREF SVNAGVTTPV STYMLTNSEL LSLINDMPIT NDQKKLMSNN VQ IVRQQSY SIMCIIKEEV LAYVVQLPLY GVIDTPCWKL HTSPLCTTNT KEGSNICLTR TDRGWYCDNA GSVSFFPQAE TCK VQSNRV FCDTMNSLTL PSEVNLCNVD IFNPKYDCKI MTSKTDVSSS VITSLGAIVS CYGKTKCTAS NKNRGIIKTF SNGC DYVSN KGVDTVSVGN TLYCVNKQEG QSLYVKGEPI INFYDPLVFP SDEFDASISQ VNEKINQSLA FIRKSDELLS AIGGY IPEA PRDGQAYVRK DGEWVLLSTF LGGLVPRGSH HHHHHSAWSH PQFEK

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Macromolecule #2: 1B6 heavy chain

MacromoleculeName: 1B6 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.707154 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LERPSETVSL TCTVSGASIN SGSYFWGWIR QPPGKGLEWV GSIHYSTTVY YNPSLKSRLT LSMDTSKNQF SLKVHAVTA ADTAVYYCAS HDWFGEPSPT YFDYWGRGTL LTVSS

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Macromolecule #3: 1A2 heavy chain

MacromoleculeName: 1A2 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.157544 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QEQLVESGGG LVKPGGSLRL SCAGSGFTFS DYDISWIRQA PGRGLEWVAY IDSSGTTIYY ADSVRGRFTI SRDTARYSVS LQLSSLRAE DTAVYYCTTK FYDYSSGTIP YYYYGLDVWG QGTRVTVSS

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Macromolecule #4: 1B6 light chain

MacromoleculeName: 1B6 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.939297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPST LSATVGDTVT ITCRASQSIS RYLAWYQQKP GKAPKLLIFR ASTLESDVPS RFSGSGSGTE FTLTITNLQP DDFATYYCQ QFNTYSPITF GQGTKLEIR

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Macromolecule #5: 1A2 light chain

MacromoleculeName: 1A2 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.389944 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPLS LSVTPGQPAS ISCKSSESLL HTDGKTYLFW YLHKPGQSPQ LLIYEVSSRF SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQGTHR PPFTFGPGTK VDIR

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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: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181211
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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