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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 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / 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: To Be Published
Title: Potent cross-neutralizing RSV/hMPV antibody targeting antigenic site V
Authors: Abu-Shmais, A.A. / Guo, L.Q. / Miller, R.J. / Janke, J.K. / Vukovich, M.J. / Lindsay, E.B. / Rush, S.A. / Wolter, R.M. / Kose, N. / Carnahan, R.H. / Crowe, J.E. / Bonami, R.H. / Mousa, J.J. ...Authors: Abu-Shmais, A.A. / Guo, L.Q. / Miller, R.J. / Janke, J.K. / Vukovich, M.J. / Lindsay, E.B. / Rush, S.A. / Wolter, R.M. / Kose, N. / Carnahan, R.H. / Crowe, J.E. / Bonami, R.H. / Mousa, J.J. / McLellan, J.S. / Georgiev, I.S.
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
Revision 1.0May 28, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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