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- PDB-8tqk: Human parainfluenza virus type 3 prefusion F trimer in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8tqk
TitleHuman parainfluenza virus type 3 prefusion F trimer in complex with rPIV3-18 Fab
Components
  • Fusion glycoprotein F0
  • Heavy chain Fab rPIV3-18
  • Light chain Fab rPIV3-28
KeywordsVIRAL PROTEIN / IMMUNE SYSTEM / viral neutralization
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHomo sapiens (human)
Human respirovirus 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsOtrelo-Cardoso, A.R. / Jardetzky, T.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI13752 United States
CitationJournal: To be published
Title: Functional and structural characteristics of human monoclonal antibodies that potently neutralize human parainfluenza virus type 3
Authors: Suryadevara, N. / Otrelo-Cardoso, A.R. / Kose, N. / Hu, Y.X. / Binshtein, E. / Wolters, R. / Drew-Bear, J. / Handal, L.S. / Carnahan, R.H. / Moscona, A. / Jardetzky, T.S. / Crowe Jr, J.E.
History
DepositionAug 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Heavy chain Fab rPIV3-18
E: Light chain Fab rPIV3-28
F: Heavy chain Fab rPIV3-18
G: Light chain Fab rPIV3-28
H: Heavy chain Fab rPIV3-18
L: Light chain Fab rPIV3-28
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)314,9749
Polymers314,9749
Non-polymers00
Water0
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 Heavy chain Fab rPIV3-18


Mass: 23959.973 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Light chain Fab rPIV3-28


Mass: 23671.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Fusion glycoprotein F0


Mass: 57360.102 Da / Num. of mol.: 3 / Mutation: Q162C, L168C, I213C, G230C, A463V, I474Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respirovirus 3 / Gene: F, KMQ_34898gpF / Production host: Homo sapiens (human) / References: UniProt: A0A059QA82

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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
1HPIV3 prefusion F trimer in complex with rPIV3-18 FabCOMPLEXall0MULTIPLE SOURCES
2Fusion glycoprotein F0COMPLEX#31RECOMBINANT
3rPIV3-18 light chainCOMPLEX#21RECOMBINANT
4rPIV3-18 heavy chainCOMPLEX#11RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Human respirovirus 311216
32Human respirovirus 311216
43Homo sapiens (human)9606
54Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCellPlasmid
21Homo sapiens (human)9606293 6eHEKPTT5
32Homo sapiens (human)9606293 6eHEKPTT5
43Cricetulus griseus (Chinese hamster)10029CHO
54Cricetulus griseus (Chinese hamster)10029CHO
Buffer solutionpH: 7.4
SpecimenConc.: 1.15 mg/ml / Embedding 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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278016 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314955
ELECTRON MICROSCOPYf_angle_d0.62120266
ELECTRON MICROSCOPYf_dihedral_angle_d4.7742037
ELECTRON MICROSCOPYf_chiral_restr0.0422388
ELECTRON MICROSCOPYf_plane_restr0.0052560

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