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- PDB-9os5: Human antibody Fab MPV498 bound to hMPV B2 post-fusion F -

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Basic information

Entry
Database: PDB / ID: 9os5
TitleHuman antibody Fab MPV498 bound to hMPV B2 post-fusion F
Components
  • Fusion glycoprotein F0
  • MPV498 Fab heavy chain
  • MPV498 Fab light chain
KeywordsIMMUNE SYSTEM / ANTIVIRAL PROTEIN / hMPV / Human respiratory disease / cryoem / human metapneumovirus
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 / membrane / Fusion glycoprotein F0
Function and homology information
Biological specieshuman metapneumovirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsGhazi Esfahani, B. / Mousa, J. / Khalil, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI143865 United States
CitationJournal: To Be Published
Title: Human metapneumovirus-specific antibodies isolated from infected children target diverse epitopes and have prophylactic efficacy in mice
Authors: Khalil, A.M. / Ghazi Esfahani, B. / Mousa, J.
History
DepositionMay 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 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: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
D: Fusion glycoprotein F0
E: Fusion glycoprotein F0
F: Fusion glycoprotein F0
G: MPV498 Fab heavy chain
J: MPV498 Fab light chain
H: MPV498 Fab heavy chain
K: MPV498 Fab light chain
I: MPV498 Fab heavy chain
L: MPV498 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,71021
Polymers376,71912
Non-polymers1,9919
Water21612
1


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

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Components

#1: Protein
Fusion glycoprotein F0


Mass: 50664.488 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human metapneumovirus / Production host: Homo sapiens (human) / References: UniProt: Q6W8S4
#2: Antibody MPV498 Fab heavy chain


Mass: 13434.042 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: Antibody MPV498 Fab light chain


Mass: 10810.029 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

ComponentName: MPV498 Fab bound to hMPV B2 post-fusion F protein / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.421 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111000 / Symmetry type: POINT
RefinementHighest resolution: 2.61 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215145
ELECTRON MICROSCOPYf_angle_d0.52120574
ELECTRON MICROSCOPYf_dihedral_angle_d6.372290
ELECTRON MICROSCOPYf_chiral_restr0.0432425
ELECTRON MICROSCOPYf_plane_restr0.0042621

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