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- EMDB-37950: Cryo-EM structure of prefusion-stabilized RSV F (DS-Cav1 sc9-10 s... -

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Basic information

Entry
Database: EMDB / ID: EMD-37950
TitleCryo-EM structure of prefusion-stabilized RSV F (DS-Cav1 sc9-10 strain: B18537) in complex with humanized nAb 5B11 (localized refinement)
Map data
Sample
  • Complex: RSV B18537 preF in complex with mAb 5B11
    • Complex: RSV pre-fusion glycoprotein
      • Protein or peptide: RSV pre-fusion glycoprotein
    • Complex: 5B11 Fab
      • Protein or peptide: 5B11 Fab Heavy Chain
      • Protein or peptide: 5B11 Fab Light Chain
Keywordsprefusion-stabilized F / Antibody / VIRAL PROTEIN
Biological speciesHuman respiratory syncytial virus B / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsLiu L / Sun H / Sun Y / 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 prefusion-stabilized RSV F (DS-Cav1 sc9-10 strain: B18537) in complex with humanized nAb 5B11 (localized refinement)
Authors: Liu L / Sun H / Sun Y / Zheng Q / Li S / Zheng Z / Xia N
History
DepositionNov 2, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37950.png

Downloads & links

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Map

FileDownload / File: emd_37950.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 400 pix.
= 311.2 Å		0.78 Å/pix.
x 400 pix.
= 311.2 Å		0.78 Å/pix.
x 400 pix.
= 311.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.0621197 - 1.5128284
Average (Standard dev.)-0.000033317345 (±0.015987245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 311.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37950_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_37950_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 B18537 preF in complex with mAb 5B11

EntireName: RSV B18537 preF in complex with mAb 5B11
Components
  • Complex: RSV B18537 preF in complex with mAb 5B11
    • Complex: RSV pre-fusion glycoprotein
      • Protein or peptide: RSV pre-fusion glycoprotein
    • Complex: 5B11 Fab
      • Protein or peptide: 5B11 Fab Heavy Chain
      • Protein or peptide: 5B11 Fab Light Chain

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Supramolecule #1: RSV B18537 preF in complex with mAb 5B11

SupramoleculeName: RSV B18537 preF in complex with mAb 5B11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human respiratory syncytial virus B

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Supramolecule #2: RSV pre-fusion glycoprotein

SupramoleculeName: RSV pre-fusion glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: 5B11 Fab

SupramoleculeName: 5B11 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2

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Macromolecule #1: 5B11 Fab Heavy Chain

MacromoleculeName: 5B11 Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.879479 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QIQLVQSGPE LKKPGASVKI SCKASGYTFT DYSMHWLKQA PGKGLKWMGW ITTETGEPTY ADDFKGRFAF SLDTSASTAY LQISSLKAE DTGVYFCARY YYGPFYWGQG TLVTVSS

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Macromolecule #2: 5B11 Fab Light Chain

MacromoleculeName: 5B11 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.763069 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRSSGNIH NFLTWYQQKP GKSPQFLVYN AKTLADGVPS RFSGSGSGTQ FTLTISSLQP EDFGIYYCQ HFWTTPYTFG GGTKVEIK

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Macromolecule #3: RSV pre-fusion glycoprotein

MacromoleculeName: RSV pre-fusion glycoprotein / type: protein_or_peptide / ID: 3
Details: The residues that would be situated between residues GLN C 98 and SER C 146 were omitted due to the absence of observable density.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human respiratory syncytial virus B
Molecular weightTheoretical: 29.179066 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGWYTSVITI ELSNIKEIKC NGTDTKVKLI KQELDKYKNA VTDLQLLMQN TPAANNRARR EAPQYMNYTI NTIKNLNVSI SKKRKRRFL GFLLGVGSAI CSGIAVCKVL HLEGEVNKIK NALLSTNKAV VSLSNGVSVL TFKVLDLKNY INNRLLPILN Q QSCRIPNI ...String:
TGWYTSVITI ELSNIKEIKC NGTDTKVKLI KQELDKYKNA VTDLQLLMQN TPAANNRARR EAPQYMNYTI NTIKNLNVSI SKKRKRRFL GFLLGVGSAI CSGIAVCKVL HLEGEVNKIK NALLSTNKAV VSLSNGVSVL TFKVLDLKNY INNRLLPILN Q QSCRIPNI ETVIEFQQMN SRLLEITREF SVNAGVTTPL STYMLTNSEL LSLINDMPIT NDQKKLMSSN VQIVRQQSYS IM CIIKEEV LAYVVQLPIY GV

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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 R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 709017
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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