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- EMDB-65394: Cryo-EM structure of RSV pre-F (strain A2) in complex with Fabs 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-65394
TitleCryo-EM structure of RSV pre-F (strain A2) in complex with Fabs 1A2 and 2D10
Map data
Sample
  • Complex: RSV pre-F protein in complex with Fabs 1A2 and 2D10
    • Complex: RSV pre-F protein
      • Protein or peptide: Fusion glycoprotein F0,Fibritin
    • Complex: 2D10 Fab
      • Protein or peptide: 2D10 heavy chain
      • Protein or peptide: 2D10 light chain
    • Complex: 1A2 Fab
      • Protein or peptide: 1A2 heavy chain
      • Protein or peptide: 1A2 light chain
KeywordsRSV / Prefusion F protein / Antibody / Viral protein/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fibritin / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A2 / Respiratory syncytial virus A2 / Homo sapiens (human) / Enterobacteria phage T6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.06 Å
AuthorsLiu L / Sun P / Li S / Zheng Q / Xia N / Zheng Z
Funding support China, 1 items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: Cryo-EM structure of RSV pre-F (strain A2) in complex with Fabs 1A2 and 2D10
Authors: Liu L / Sun P / Li S / Zheng Q / Xia N
History
DepositionJul 17, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65394.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 392 pix.
= 254.8 Å		0.65 Å/pix.
x 392 pix.
= 254.8 Å		0.65 Å/pix.
x 392 pix.
= 254.8 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: 0.1
Minimum - Maximum-0.15151729 - 4.5877476
Average (Standard dev.)0.0055956487 (±0.087670945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 254.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65394_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_65394_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 2D10

EntireName: RSV pre-F protein in complex with Fabs 1A2 and 2D10
Components
  • Complex: RSV pre-F protein in complex with Fabs 1A2 and 2D10
    • Complex: RSV pre-F protein
      • Protein or peptide: Fusion glycoprotein F0,Fibritin
    • Complex: 2D10 Fab
      • Protein or peptide: 2D10 heavy chain
      • Protein or peptide: 2D10 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 2D10

SupramoleculeName: RSV pre-F protein in complex with Fabs 1A2 and 2D10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human 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: 2D10 Fab

SupramoleculeName: 2D10 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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Supramolecule #4: 1A2 Fab

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

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Macromolecule #1: Fusion glycoprotein F0,Fibritin

MacromoleculeName: Fusion glycoprotein F0,Fibritin / type: protein_or_peptide / ID: 1
Details: Sequence reference for Respiratory syncytial virus A2 is not available at the time of biocuration. Current sequence reference is from UniProt id P03420.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T6 (virus)
Molecular weightTheoretical: 63.340523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ATMELLILKA NAITTILTAV TFCFASGQNI TEEFYQSTCS AVSKGYLGAL RTGWYTSVIT IELSNIKEIK CNGTDAKVKL IKQELDKYK NAVTDLQLLM QSTPPTNNRA RRELPRFMNY TLNNAKKTNV TLSKKRKRRF LGFLLGSGSA ICSGVAVCKV L HLEGEVNK ...String:
ATMELLILKA NAITTILTAV TFCFASGQNI TEEFYQSTCS AVSKGYLGAL RTGWYTSVIT IELSNIKEIK CNGTDAKVKL IKQELDKYK NAVTDLQLLM QSTPPTNNRA RRELPRFMNY TLNNAKKTNV TLSKKRKRRF LGFLLGSGSA ICSGVAVCKV L HLEGEVNK IKSALLSTNK AVVSLSNGVS VLTFKVLDLK NYIDKQLLPI LNKQSCSIPN IETVIEFQQK NNRLLEITRE FS VNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YSIMCIIKEE VLAYVVQLPL YGVIDTPCWK LHT SPLCTT NTKEGSNICL TRTDRGWYCD NAGSVSFFPQ AETCKVQSNR VFCDTMNSLT LPSEVNLCNV DIFNPKYDCK IMTS KTDVS SSVITSLGAI VSCYGKTKCT ASNKNRGIIK TFSNGCDYVS NKGVDTVSVG NTLYCVNKQE GQSLYVKGEP IINFY DPLV FPSDEFDASI SQVNEKINQS LAFIRKSDEL LSAIGGYIPE APRDGQAYVR KDGEWVLLST FLGGLVPRGS HHHHHH SAW SHPQFEK

UniProtKB: Fusion glycoprotein F0, Fibritin

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Macromolecule #2: 2D10 heavy chain

MacromoleculeName: 2D10 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.60579 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGGSIG FDYWSWIRQS PEKGLEWIGY VYYSGDTNYN PSLESRLTIS VDTSRSQFSL RLSSVTAAD TAVYYCARFG SGGFDSWGQG TLVTVSS

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Macromolecule #3: 2D10 light chain

MacromoleculeName: 2D10 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.510651 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELKQPPSV SVSPGQTARI TCSGDALARH FAHWYQQKPG QAPVLLIYQG TERPSRVPER FSGSNSGTTV TLTISGVQAE DEADYYCQS ADNSGTFVFG TGTKVTVL

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Macromolecule #4: 1A2 heavy chain

MacromoleculeName: 1A2 heavy chain / type: protein_or_peptide / ID: 4 / 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 #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 / 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: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 601347
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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