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- PDB-8f6x: cryo-EM structure of a structurally designed Human metapneumoviru... -

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Basic information

Entry
Database: PDB / ID: 8f6x
Titlecryo-EM structure of a structurally designed Human metapneumovirus F protein in complex with antibody MPE8
Components
  • MPE8 Single chain variable fragment
  • Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / metapneumovirus / HMPV / F protein / antibody / MPE8 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / 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 metapneumovirus
Escherichia phage T2 (virus)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsZhou, T. / Kwong, P.D. / Morano, N.C. / Ou, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: cryo-EM structure of a structurally designed Human metapneumovirus F protein in complex with antibody MPE8
Authors: Ou, L. / Kwong, P.D.
History
DepositionNov 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin
B: Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin
C: Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin
D: MPE8 Single chain variable fragment
E: MPE8 Single chain variable fragment
F: MPE8 Single chain variable fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,3759
Polymers266,7116
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin


Mass: 56891.637 Da / Num. of mol.: 3
Mutation: several mutations introduced to structurally redesign the F protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus, (gene. exp.) Escherichia phage T2 (virus)
Plasmid: pVRC8400 / Gene: wac / Cell (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: G3KCK8, UniProt: A0A2Z5WL46
#2: Antibody MPE8 Single chain variable fragment


Mass: 32012.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell (production host): 293F / Production host: Homo sapiens (human)
#3: 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.: 3
Source method: isolated from a genetically manipulated source
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
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: Purified complex of HMPV F with single chain Fv MPE8 / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.266 MDa / Experimental value: NO
Buffer solutionpH: 7.4
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 58.06 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: Leginon / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 192259 / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215210
ELECTRON MICROSCOPYf_angle_d0.48920628
ELECTRON MICROSCOPYf_dihedral_angle_d4.0132154
ELECTRON MICROSCOPYf_chiral_restr0.0442391
ELECTRON MICROSCOPYf_plane_restr0.0042652

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