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Yorodumi- PDB-2hmg: REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hmg | ||||||||||||
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Title | REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / INFLUENZA VIRUS HEMAGGLUTININ | ||||||||||||
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 / Resolution: 3 Å | ||||||||||||
Authors | Weis, W.I. / Bruenger, A.T. / Skehel, J.J. / Wiley, D.C. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1990 Title: Refinement of the influenza virus hemagglutinin by simulated annealing. Authors: Weis, W.I. / Brunger, A.T. / Skehel, J.J. / Wiley, D.C. #1: Journal: Nature / Year: 1988 Title: Structure of the Influenza Virus Haemagglutinin Complexed with its Receptor, Sialic Acid Authors: Weis, W. / Brown, J.H. / Cusack, S. / Paulson, J.C. / Skehel, J.J. / Wiley, D.C. #2: Journal: Nature / Year: 1984 Title: Three-Dimensional Structure of an Antigenic Mutant of the Influenza Virus Haemagglutinin Authors: Knossow, M. / Daniels, R.S. / Douglas, A.R. / Skehel, J.J. / Wiley, D.C. #3: Journal: Nature / Year: 1981 Title: Structure of the Haemagglutinin Membrane Glycoprotein of Influenza Virus at 3 Angstroms Resolution Authors: Wilson, I.A. / Skehel, J.J. / Wiley, D.C. #4: Journal: Nature / Year: 1981 Title: Structural Identification of the Antibody-Binding Sites of Hong Kong Influenza Haemagglutinin and Their Involvement in Antigenic Variation Authors: Wiley, D.C. / Wilson, I.A. / Skehel, J.J. #5: Journal: J.Mol.Biol. / Year: 1977 Title: Crystallization and X-Ray Diffraction Studies on the Haemagglutinin Glycoprotein from the Membrane of Influenza Virus Authors: Wiley, D.C. / Skehel, J.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hmg.cif.gz | 298.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hmg.ent.gz | 249 KB | Display | PDB format |
PDBx/mmJSON format | 2hmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hmg_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2hmg_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2hmg_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 2hmg_validation.cif.gz | 76.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/2hmg ftp://data.pdbj.org/pub/pdb/validation_reports/hm/2hmg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO A 55, PRO C 55, PRO E 55 ARE CIS-PROLINES. 2: A TEMPERATURE FACTOR OF 65.0 OR LARGER SIGNIFIES AN ATOM WHOSE COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA. | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details |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|
-Components
#1: Protein | Mass: 36123.496 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Strain: (A/HongKong/19/68(H3N2)) / Variant: (A/HongKong/19/68(H3N2)) / References: UniProt: P03437 #2: Protein | Mass: 20212.350 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Strain: (A/HongKong/19/68(H3N2)) / Variant: (A/HongKong/19/68(H3N2)) / References: UniProt: P03437 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS pH: 7.5 / Method: unknown / Details: Wilson, I.A., (1981) Nature, 289, 366. | |||||||||||||||
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Components of the solutions | *PLUS
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-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.222 / Highest resolution: 3 Å Details: A TEMPERATURE FACTOR OF 65.0 OR LARGER SIGNIFIES AN ATOM WHOSE COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.222 / Lowest resolution: 7 Å / Num. reflection obs: 67242 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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