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- PDB-9cb1: Cryo-EM Structure of the Human Neutralizing Antibody 5-1 in Compl... -

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Basic information

Entry
Database: PDB / ID: 9cb1
TitleCryo-EM Structure of the Human Neutralizing Antibody 5-1 in Complex with Prefusion Human Metapneumovirus F Glycoprotein
Components
  • 5-1 Fab Heavy Chain Variable Domain
  • 5-1 Fab Light Chain Variable Domain
  • Fusion glycoprotein F0
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hMPV F / 5-1 antibody / antibody / VIRAL PROTEIN-IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHomo sapiens (human)
human metapneumovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.24 Å
AuthorsGuo, L.Q. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: Cell Rep Med / Year: 2026
Title: A potently neutralizing and protective human antibody targeting antigenic site V on RSV and hMPV fusion glycoprotein.
Authors: Alexandra A Abu-Shmais / Luqiang Guo / Ahmed Magdy Khalil / Sabina E Leonard / Rose J Miller / Alexis K Janke / Matthew J Vukovich / Lindsay E Bass / Yukthi P Suresh / Scott A Rush / Rachael ...Authors: Alexandra A Abu-Shmais / Luqiang Guo / Ahmed Magdy Khalil / Sabina E Leonard / Rose J Miller / Alexis K Janke / Matthew J Vukovich / Lindsay E Bass / Yukthi P Suresh / Scott A Rush / Rachael M Wolters / Nurgun Kose / Robert H Carnahan / James E Crowe / Rachel H Bonami / Jarrod J Mousa / Jason S McLellan / Ivelin S Georgiev /
Abstract: Human respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are frequent drivers of morbidity and mortality in susceptible populations. The primary target of neutralizing antibodies is ...Human respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are frequent drivers of morbidity and mortality in susceptible populations. The primary target of neutralizing antibodies is the fusion (F) glycoprotein on the surface of the RSV and hMPV virion. As a result of the structural conservation between RSV and hMPV F, three antigenic regions are known to induce cross-neutralizing responses: sites III, IV, and V. Leveraging LIBRA-seq, we identify five RSV/hMPV cross-reactive human antibodies. One antibody, RM 5-1, potently neutralizes all tested viruses from the major subgroups of RSV and hMPV and provides protection against RSV and hMPV in a mouse challenge model. Structural analysis reveals that RM 5-1 utilizes an uncommon genetic signature to bind an epitope that spans sites Ø, II, and V. These findings highlight the molecular and structural elements influencing RSV and hMPV cross-reactivity as well as the potential of antibody RM 5-1 for translational development.
History
DepositionJun 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0May 28, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-1 Fab Heavy Chain Variable Domain
B: 5-1 Fab Heavy Chain Variable Domain
C: 5-1 Fab Heavy Chain Variable Domain
D: 5-1 Fab Light Chain Variable Domain
E: 5-1 Fab Light Chain Variable Domain
F: 5-1 Fab Light Chain Variable Domain
G: Fusion glycoprotein F0
H: Fusion glycoprotein F0
I: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,01412
Polymers321,7419
Non-polymers1,2733
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody 5-1 Fab Heavy Chain Variable Domain


Mass: 23170.996 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Expi293F / Production host: Homo sapiens (human)
#2: Antibody 5-1 Fab Light Chain Variable Domain


Mass: 23586.084 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Fusion glycoprotein F0 / F-DsCavEs2-IPDS


Mass: 60489.930 Da / Num. of mol.: 3 / Mutation: multiple
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human metapneumovirus / Production host: Homo sapiens (human) / References: UniProt: H6X1Z1
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1The protein complex of hMPV F-DsCavEs2-IPDS and 5-1 FabCOMPLEX#1-#30MULTIPLE SOURCES
2hMPV F-DsCavEs2-IPDS TrimerCOMPLEX#31RECOMBINANT
35-1 Fab Heavy chain Variable DomainCOMPLEX#11RECOMBINANT
45-1 Fab Light Chain Variable DomainCOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12human metapneumovirus162145
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Buffer solutionpH: 7.4 / Details: PBS, pH 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 13.2 sec. / Electron dose: 48.64 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18483 / Symmetry type: POINT
RefinementCross valid method: NONE

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