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Yorodumi- PDB-7qa4: Crystal structure of stabilized H3N2 A/Hong Kong/1/1968 Hemagglut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qa4 | ||||||
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Title | Crystal structure of stabilized H3N2 A/Hong Kong/1/1968 Hemagglutinin at 2.2 Angstrom | ||||||
Components | Hemagglutinin | ||||||
Keywords | VIRAL PROTEIN / Influenza / Hemagglutinin / Stabilized / Fusion protein / UNKNOWN FUNCTION | ||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Milder, F.J. / Langedijk, J.P.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Universal stabilization of the influenza hemagglutinin by structure-based redesign of the pH switch regions. Authors: Milder, F.J. / Jongeneelen, M. / Ritschel, T. / Bouchier, P. / Bisschop, I.J.M. / de Man, M. / Veldman, D. / Le, L. / Kaufmann, B. / Bakkers, M.J.G. / Juraszek, J. / Brandenburg, B. / Langedijk, J.P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qa4.cif.gz | 211 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qa4.ent.gz | 176.3 KB | Display | PDB format |
PDBx/mmJSON format | 7qa4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qa4_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7qa4_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7qa4_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 7qa4_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/7qa4 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/7qa4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57131.680 Da / Num. of mol.: 1 / Fragment: Hemagglutinin Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2) Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q91MA7 |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
-Non-polymers , 2 types, 135 molecules
#6: Chemical | ChemComp-NO3 / |
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#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 20.00 %w/v PEG 3350, 0.2 M LiNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999924 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999924 Å / Relative weight: 1 |
Reflection | Resolution: 2.192→108.96 Å / Num. obs: 31315 / % possible obs: 100 % / Redundancy: 25.6 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.192→108.96 Å / Redundancy: 26.2 % / Rmerge(I) obs: 2.977 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 31315 / Rsym value: 2.977 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: none Resolution: 2.19→108.96 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 13.987 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 158.29 Å2 / Biso mean: 66.571 Å2 / Biso min: 39.58 Å2
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Refinement step | Cycle: final / Resolution: 2.19→108.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.192→2.249 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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