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- PDB-4hmg: REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hmg | |||||||||
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Title | REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING | |||||||||
![]() | (HEMAGGLUTININ, CHAIN ...) x 2 | |||||||||
![]() | VIRAL PROTEIN / INFLUENZA VIRUS HEMAGGLUTININ | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Weis, W.I. / Bruenger, A.T. / Skehel, J.J. / Wiley, D.C. | |||||||||
![]() | ![]() Title: Refinement of the influenza virus hemagglutinin by simulated annealing. Authors: Weis, W.I. / Brunger, A.T. / Skehel, J.J. / Wiley, D.C. #1: ![]() Title: Structure of the Influenza Virus Haemagglutinin Complexes with its Receptor, Sialic Acid Authors: Weis, W. / Brown, J.H. / Cusack, S. / Paulson, J.C. / Skehel, J.J. / Wiley, D.C. #2: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 299.7 KB | Display | ![]() |
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PDB format | ![]() | 250.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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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|
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Components
-HEMAGGLUTININ, CHAIN ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 36080.430 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 20212.350 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 3 types, 18 molecules ![](data/chem/img/SIA.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 33 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | *PLUS pH: 7.5 / Method: microdialysisDetails: referred to 'Weis, W.', (1988) Nature, 333, 426-431 | ||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 7 Å / Num. obs: 64062 / % possible obs: 70.8 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.125 |
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Processing
Software | Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.231 / 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.231 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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