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Yorodumi- PDB-8tqk: Human parainfluenza virus type 3 prefusion F trimer in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tqk | ||||||
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Title | Human parainfluenza virus type 3 prefusion F trimer in complex with rPIV3-18 Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN / IMMUNE SYSTEM / viral neutralization | ||||||
Function / homology | Precursor 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 species | Homo sapiens (human) Human respirovirus 3 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Otrelo-Cardoso, A.R. / Jardetzky, T.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tqk.cif.gz | 693.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tqk.ent.gz | 576.8 KB | Display | PDB format |
PDBx/mmJSON format | 8tqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tqk_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8tqk_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8tqk_validation.xml.gz | 66.6 KB | Display | |
Data in CIF | 8tqk_validation.cif.gz | 100.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/8tqk ftp://data.pdbj.org/pub/pdb/validation_reports/tq/8tqk | HTTPS FTP |
-Related structure data
Related structure data | 41506MC 8tqiC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Antibody | 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 | 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 | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||
Specimen | Conc.: 1.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278016 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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