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Yorodumi- PDB-1ken: INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH AN ANTIBODY THAT PRE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ken | |||||||||
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Title | INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH AN ANTIBODY THAT PREVENTS THE HEMAGGLUTININ LOW PH FUSOGENIC TRANSITION | |||||||||
Components |
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Keywords | Viral protein/Immune system / HEMAGGLUTININ / ENVELOPE PROTEIN / GLYCOPROTEIN / Viral protein-Immune system COMPLEX | |||||||||
Function / homology | Function and homology information Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / B cell differentiation / antigen binding / viral budding from plasma membrane / positive regulation of immune response / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / defense response to bacterium / external side of 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 / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Influenza A virus Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Barbey-Martin, C. / Gigant, B. / Bizebard, T. / Calder, L.J. / Wharto, S.A. / Skehel, J.J. / Knossow, M. | |||||||||
Citation | Journal: VIROLOGY / Year: 2002 Title: An Antibody that Prevents the Hemagglutinin Low pH Fusogenic Transition Authors: Barbey-Martin, C. / Gigant, B. / Bizebard, T. / Calder, L.J. / Wharton, S.A. / Skehel, J.J. / Knossow, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: A Neutralizing Antibody Fab-Influenza Haemagglutinin Complex with an Unprecedented 2:1 Stoichiometry:Characterization and Crystallization Authors: Gigant, B. / Barbey-Martin, C. / Bizebard, T. / Fleury, D. / Daniels, R. / Skehel, J.J. / Knossow, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ken.cif.gz | 420.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ken.ent.gz | 346.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ken.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ken_validation.pdf.gz | 672.4 KB | Display | wwPDB validaton report |
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Full document | 1ken_full_validation.pdf.gz | 916.9 KB | Display | |
Data in XML | 1ken_validation.xml.gz | 80.1 KB | Display | |
Data in CIF | 1ken_validation.cif.gz | 115.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/1ken ftp://data.pdbj.org/pub/pdb/validation_reports/ke/1ken | 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
#1: Protein | Mass: 36065.457 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Influenza A virus (A/X-31(H3N2)) / Genus: Influenzavirus A / Species: Influenza A virus / Strain: X31 / References: GenBank: 324239, UniProt: P03438*PLUS #2: Protein | Mass: 20212.350 Da / Num. of mol.: 3 / Fragment: FAB fragment of antibody / Source method: isolated from a natural source / Details: BROMELAIN DIGESTED / Source: (natural) Influenza A virus (A/X-31(H3N2)) / Genus: Influenzavirus A / Species: Influenza A virus / Strain: X31 / References: UniProt: P03437 #3: Antibody | Mass: 23275.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 7209188, UniProt: P01837*PLUS #4: Antibody | Mass: 24352.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 17977852, UniProt: P01869*PLUS #5: Polysaccharide | Source method: isolated from a genetically manipulated source Has protein modification | Y | |
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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: 4.14 Å3/Da / Density % sol: 70.32 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: peg 20000, calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 KDetails: Gigant, B., (2000) Acta Crystallogr., Sect.D, 56, 1067. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→25 Å / Num. obs: 54923 / % possible obs: 98.2 % / Redundancy: 3.9 % / Rsym value: 0.128 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3.5→3.7 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.42 / % possible all: 98.2 |
Reflection | *PLUS Rmerge(I) obs: 0.128 |
Reflection shell | *PLUS Lowest resolution: 3.69 Å / % possible obs: 98.2 % / Rmerge(I) obs: 0.423 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→25 Å / Rfactor Rfree error: 0.006 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5 Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL, DUE TO THE LIMITED (3.5 ANGSTROMS) RESOLUTION. THE OVERALL COORDINATE ERROR IS ESTIMATED TO BE APPROXIMATELY 0.45-0.60 ANGSTROMS, ...Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL, DUE TO THE LIMITED (3.5 ANGSTROMS) RESOLUTION. THE OVERALL COORDINATE ERROR IS ESTIMATED TO BE APPROXIMATELY 0.45-0.60 ANGSTROMS, BUT THE ERROR IS HIGHER IN REGIONS HAVING HIGH TEMPERATURE FACTORS. PRECISE ASSIGNMENT OF HYDROGEN BONDS, OTHER CONTACTS AND SECONDARY STRUCTURAL ELEMENTS AT THIS RESOLUTION IS NOT POSSIBLE. ATOMS WITH TEMPERATURE FACTORS GREATER THAN 65 ANGSTROMS SQUARED SHOULD BE INTERPRETED WITH CAUTION. RESIDUES 1-8 OF HA1 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.7473 Å2 / ksol: 0.206359 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 47.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.72 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor obs: 0.256 / Rfactor Rfree: 0.324 / Rfactor Rwork: 0.256 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.295 |