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- EMDB-59533: Immune complex comprising the HRSV preF trimer (SC-DM) and the mo... -

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Basic information

Entry
Database: EMDB / ID: EMD-59533
TitleImmune complex comprising the HRSV preF trimer (SC-DM) and the monoclonal antibody Lor69 - Obtained by cryo-EM
Map dataMain map of the prefusion HRSV trimer (SC-DM) in complex with the Lor69 monoclonal antibody.
Sample
  • Complex: Monoclonal antibody Lor69 complex with HRSV preF trimer (SC-DM).
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Lor69 Heavy Chain
    • Protein or peptide: Lor69 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntigen / antibody / complex / RSV / VIRAL PROTEIN
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
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesRespiratory syncytial virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsOls S / Cerveira RA / Borst AJ / Bermudez-Mendez E / Gegenfurtner F / Eray E / Weidle C / Miranda MC / Peng Z / Carr KD ...Ols S / Cerveira RA / Borst AJ / Bermudez-Mendez E / Gegenfurtner F / Eray E / Weidle C / Miranda MC / Peng Z / Carr KD / Skotheim R / Kochmann J / Brunette N / Lenart K / Hanke L / Karlsson Hedestam GB / Perez L / Antanasijevic A / King NP / Lore K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36621 United States
CitationJournal: bioRxiv / Year: 2026
Title: Distinct mechanisms of neutralization by antibodies targeting a conserved pneumovirus F epitope.
Authors: Sebastian Ols / Rodrigo Arcoverde Cerveira / Andrew J Borst / Erick Bermúdez-Méndez / Florian Gegenfurtner / Elise Eray / Connor Weidle / Marcos C Miranda / Zhitong Peng / Kenneth D Carr / ...Authors: Sebastian Ols / Rodrigo Arcoverde Cerveira / Andrew J Borst / Erick Bermúdez-Méndez / Florian Gegenfurtner / Elise Eray / Connor Weidle / Marcos C Miranda / Zhitong Peng / Kenneth D Carr / Rebecca Skotheim / Jana Kochmann / Natalie Brunette / Klara Lenart / Leo Hanke / Gunilla B Karlsson Hedestam / Laurent Perez / Aleksandar Antanasijevic / Neil P King / Karin Loré /
Abstract: Pneumoviruses cause seasonal outbreaks leading to hospitalizations of vulnerable populations such as infants and the elderly. Cross-neutralizing antibodies targeting viral fusion have been isolated ...Pneumoviruses cause seasonal outbreaks leading to hospitalizations of vulnerable populations such as infants and the elderly. Cross-neutralizing antibodies targeting viral fusion have been isolated from infected individuals, but their elicitation and mechanisms of action remain understudied. Here, we describe two vaccine-elicited antibody classes, LOR24 and LOR69, that bind an overlapping epitope, and identify the somatic mutations that endow their breadth and potency, respectively. Cryo-electron microscopy structures of both antibodies bound to the HRSV fusion (F) protein show binding modes distinct from each other and from the previously described cross-neutralizing antibody MPE8, yet they all use similar motifs for binding. Complementary and electron microscopy experiments show that these antibodies either lock prefusion F as a trimer, arrest F in a monomeric or intermediate state, or promote the transition to the postfusion conformation. This work sheds light on mechanisms of pneumovirus neutralization and the elicitation of cross-neutralizing antibody responses.
History
DepositionAug 21, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59533.png

Downloads & links

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Map

FileDownload / File: emd_59533.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map of the prefusion HRSV trimer (SC-DM) in complex with the Lor69 monoclonal antibody.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 277.8 Å		0.93 Å/pix.
x 300 pix.
= 277.8 Å		0.93 Å/pix.
x 300 pix.
= 277.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.013168515 - 0.028339379
Average (Standard dev.)0.00001098906 (±0.0007612965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 277.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_59533_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the prefusion HRSV trimer...

Fileemd_59533_half_map_1.map
AnnotationHalf map 1 of the prefusion HRSV trimer (SC-DM) in complex with the Lor69 monoclonal antibody.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the prefusion HRSV trimer...

Fileemd_59533_half_map_2.map
AnnotationHalf map 2 of the prefusion HRSV trimer (SC-DM) in complex with the Lor69 monoclonal antibody.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Monoclonal antibody Lor69 complex with HRSV preF trimer (SC-DM).

EntireName: Monoclonal antibody Lor69 complex with HRSV preF trimer (SC-DM).
Components
  • Complex: Monoclonal antibody Lor69 complex with HRSV preF trimer (SC-DM).
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Lor69 Heavy Chain
    • Protein or peptide: Lor69 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Monoclonal antibody Lor69 complex with HRSV preF trimer (SC-DM).

SupramoleculeName: Monoclonal antibody Lor69 complex with HRSV preF trimer (SC-DM).
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Respiratory syncytial virus

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Details: SC-DM variant / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus
Molecular weightTheoretical: 57.338434 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKKIKCN GTDAKIKLIK QELDKYKNA VTELQLLMQS TPATNNQARG SGSGRSLGFL LGVGSAIASG VAVSKVLHLE GEVNKIKSAL LSTNKAVVSL S NGVSVLTS ...String:
MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKKIKCN GTDAKIKLIK QELDKYKNA VTELQLLMQS TPATNNQARG SGSGRSLGFL LGVGSAIASG VAVSKVLHLE GEVNKIKSAL LSTNKAVVSL S NGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSIPNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL IN DMPITND QKKLMSNNVQ IVRQQSYSIM SIIKEEVLAY VVQLPLYGVI DTPCWKLHTS PLCTTNTKEG SNICLTRTDR GWY CDNAGS VSFFPQAETC KVQSNRVFCD TMNSLTLPSE VNLCNVDIFN PKYDCKIMTS KTDVSSSVIT SLGAIVSCYG KTKC TASNK NRGIIKTFSN GCDYVSNKGV DTVSVGNTLY YVNKQEGKSL YVKGEPIINF YDPLVFPSDE FDASISQVNE KINQS LAFI RKSDELLSAI GGYIPEAPRD GQAYVRKDGE WVLLSTFL

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Lor69 Heavy Chain

MacromoleculeName: Lor69 Heavy Chain / type: protein_or_peptide / ID: 2 / Details: Heavy chain / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.104435 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLQLQESGPG LVKSSETLSL TCAVSGDSIR SNFWSWIRQA PGKGLEWIGY IYGTGSSTNY NPSLESRVTL SVDTSKNHLS LKLSSVTAA DTAVYYCARD RGYSGYSPQD FWGQGVLVTV SS

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Macromolecule #3: Lor69 Light Chain

MacromoleculeName: Lor69 Light Chain / type: protein_or_peptide / ID: 3 / Details: Light chain / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.822156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDTVT ITCRASQGIN IYVAWYQQKP GKAPRPLIYY ASTLETGVPS RFSGRGSGTD FTLTISSLQP EDFATYHCQ QHRSYPWTFG QGTKLEIK

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
Component:
ConcentrationFormulaName
137.0 mMNaClSodium Chloride
2.7 mMKClPotassium Chloride
10.0 mMNa2HPO4Disodium hydrigen phosphate
1.8 mMKH2PO4Potassium dihydrogen

Details: PBS 1x
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
Details: Blot force of 0, wait time of 10s, blot time of 4-6s.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5373 / Average electron dose: 40.0 e/Å2
Details: 2782 micrographs collected untilted and 2591 micrographs collected with a 30 degree tilt.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: OTHER

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Image processing

Particle selectionNumber selected: 361187
CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Low-pass filtered map of the SOSIP complex
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 128395
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0) / Details: 3D auto refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0) / Details: 3D auto refinement
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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