+Open data
-Basic information
Entry | Database: PDB / ID: 1rvt | |||||||||
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Title | 1930 H1 Hemagglutinin in complex with LSTC | |||||||||
Components | (hemagglutinin) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Hemagglutinin / Influenza A virus | |||||||||
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 | unidentified influenza virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Skehel, J.J. / Gamblin, S.J. / Haire, L.F. / Russell, R.J. / Stevens, D.J. / Xiao, B. / Ha, Y. / Vasisht, N. / Steinhauer, D.A. / Daniels, R.S. | |||||||||
Citation | Journal: Science / Year: 2004 Title: The structure and receptor binding properties of the 1918 influenza hemagglutinin. Authors: Gamblin, S.J. / Haire, L.F. / Russell, R.J. / Stevens, D.J. / Xiao, B. / Ha, Y. / Vasisht, N. / Steinhauer, D.A. / Daniels, R.S. / Elliot, A. / Wiley, D.C. / Skehel, J.J. | |||||||||
History |
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Remark 999 | Author states that the sequence of this protein is correct and there is no matched sequence ...Author states that the sequence of this protein is correct and there is no matched sequence database available. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rvt.cif.gz | 307.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rvt.ent.gz | 248.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/1rvt ftp://data.pdbj.org/pub/pdb/validation_reports/rv/1rvt | HTTPS FTP |
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-Related structure data
Related structure data | 1ru7SC 1ruyC 1ruzC 1rv0C 1rvxC 1rvzC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 6 molecules HJLIKM
#1: Protein | Mass: 36061.383 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Bromelain digestion / Source: (natural) unidentified influenza virus / Strain: A/Swine/Iowa/15/30 / References: UniProt: Q82500*PLUS #2: Protein | Mass: 18180.053 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Bromelain digestion / Source: (natural) unidentified influenza virus / Strain: A/Swine/Iowa/15/30 / References: UniProt: Q82500*PLUS |
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-Sugars , 3 types, 6 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 1 types, 592 molecules
#6: 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: 4.45 Å3/Da / Density % sol: 72.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 5K MME, TrisHCl, Sodium citrate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.9794 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 97698 / Num. obs: 97348 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.2 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RU7 Resolution: 2.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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