+Open data
-Basic information
Entry | Database: PDB / ID: 3lzg | |||||||||
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Title | Crystal structure of a 2009 H1N1 influenza virus hemagglutinin | |||||||||
Components | (Hemagglutinin, ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / viral envelope protein / hemagglutinin / viral fusion protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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 Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Xu, R. / Wilson, I.A. | |||||||||
Citation | Journal: Science / Year: 2010 Title: Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus. Authors: Xu, R. / Ekiert, D.C. / Krause, J.C. / Hai, R. / Crowe, J.E. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lzg.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3lzg.ent.gz | 994.9 KB | Display | PDB format |
PDBx/mmJSON format | 3lzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/3lzg ftp://data.pdbj.org/pub/pdb/validation_reports/lz/3lzg | HTTPS FTP |
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-Related structure data
Related structure data | 3lzfC 1rd8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Hemagglutinin, ... , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 36543.238 Da / Num. of mol.: 6 / Fragment: Ectodomain HA1, residues 18-344 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/California/04/2009 / Gene: HA, hemagglutinin / Plasmid: pFASTbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C3W5S1 #2: Protein | Mass: 20278.383 Da / Num. of mol.: 6 / Fragment: Ectodomain HA2, residues 345-520 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/California/04/2009 / Gene: HA, hemagglutinin / Plasmid: pFastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C3W5S1 |
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-Sugars , 4 types, 6 molecules
#3: 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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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: 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 #6: Sugar | |
-Non-polymers , 1 types, 463 molecules
#7: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.4 % |
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Crystal grow | Temperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 27% PEG-MME 2000, 0.1M Tris pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.03317 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 26, 2009 Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45 Å / Num. all: 102429 / Num. obs: 93210 / % possible obs: 91 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 61.66 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 7120 / Rsym value: 0.375 / % possible all: 69.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RD8 Resolution: 2.6→45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 65.71 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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