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Yorodumi- PDB-8dim: CryoEM structure of Influenza A virus A/Ohio/09/2015 hemagglutini... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dim | ||||||
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Title | CryoEM structure of Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / NIAID / hemagglutinin stalk binding antibody / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Biological species | Influenza A virus Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: CryoEM structure of Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab Authors: Yang, M. / Edwards, T.E. / Horanyi, P.S. / Lorimer, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dim.cif.gz | 778.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dim.ent.gz | 521.6 KB | Display | PDB format |
PDBx/mmJSON format | 8dim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dim_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8dim_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8dim_validation.xml.gz | 77.9 KB | Display | |
Data in CIF | 8dim_validation.cif.gz | 115.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/8dim ftp://data.pdbj.org/pub/pdb/validation_reports/di/8dim | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Antibody , 2 types, 6 molecules BEHCFI
#2: Antibody | Mass: 27066.621 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): HEK293e #3: Antibody | Mass: 25514.395 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): hek293e |
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-Protein / Non-polymers , 2 types, 21 molecules ADG
#1: Protein | Mass: 64428.137 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Ohio/09/2015 / Cell line (production host): Sf9 / Production host: Trichoplusia ni (cabbage looper) #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 12 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | Y |
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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 | Name: Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | |||||||||||||||
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Molecular weight | Value: 0.45 MDa / Experimental value: NO | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2.3 sec. / Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 12095 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 367154 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 120.6 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6UYN Accession code: 6UYN / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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