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Yorodumi- PDB-1qfu: INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qfu | |||||||||
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Title | INFLUENZA VIRUS HEMAGGLUTININ COMPLEXED WITH A NEUTRALIZING ANTIBODY | |||||||||
Components |
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Keywords | Viral protein/Immune system / COMPLEX (HEMAGGLUTININ-IMMMUNOGLOBULIN) / HEMAGGLUTININ / IMMUNOGLOBULIN / 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 / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / 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 / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / viral budding from plasma membrane / complement activation, classical pathway / antigen binding / 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 / immune response / 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 / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Influenza A virus Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Fleury, D. / Gigant, B. / Bizebard, T. / Daniels, R.S. / Skehel, J.J. / Knossow, M. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: A complex of influenza hemagglutinin with a neutralizing antibody that binds outside the virus receptor binding site. Authors: Fleury, D. / Barrere, B. / Bizebard, T. / Daniels, R.S. / Skehel, J.J. / Knossow, M. #1: Journal: Nature / Year: 1995 Title: Structure of influenza virus haemagglutinin complexed with a neutralizing antibody. Authors: Bizebard, T. / Gigant, B. / Rigolet, P. / Rasmussen, B. / Diat, O. / Bosecke, P. / Wharton, S.A. / Skehel, J.J. / Knossow, M. #2: Journal: Proteins / Year: 1995 Title: Crystallization and preliminary X-ray diffraction studies of complexes between an influenza hemagglutinin and Fab fragments of two different monoclonal antibodies. Authors: Gigant, B. / Fleury, D. / Bizebard, T. / Skehel, J.J. / Knossow, M. #3: Journal: Nature / Year: 1981 Title: Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 A resolution. Authors: Wilson, I.A. / Skehel, J.J. / Wiley, D.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qfu.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qfu.ent.gz | 157.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qfu_validation.pdf.gz | 564.1 KB | Display | wwPDB validaton report |
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Full document | 1qfu_full_validation.pdf.gz | 601.5 KB | Display | |
Data in XML | 1qfu_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 1qfu_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/1qfu ftp://data.pdbj.org/pub/pdb/validation_reports/qf/1qfu | 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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Details | THERE IS ONE MONOMER OF THE TRIMERIC HEMAGGLUTININ MOLECULE IN THE ASYMMETRIC UNIT, AND EACH MONOMER IS COMPLEXED WITH ONE FAB FRAGMENT. THE MONOMER OF HEMAGGLUTININ CONSISTS OF TWO CHAINS, IDENTIFIED AS HA1 AND HA2. CHAINS HA1 AND HA2 HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*, RESPECTIVELY. IN THE VIRUS, CHAIN HA1 CONSISTS OF 328 RESIDUES AND CHAIN. HA2 CONSISTS OF 220 RESIDUES. HEMAGGLUTININ MAY BE SOLUBILIZED FROM THE VIRAL MEMBRANE BY BROMELAIN DIGESTION, WHICH REMOVES THE C-TERMINAL HYDROPHOBIC (ANCHORING) DOMAIN. FROM CHAIN HA2. AFTER BROMELAIN DIGESTION CHAIN HA2 CONSISTS OF 175 RESIDUES, AS PRESENTED IN THIS ENTRY. |
-Components
-PROTEIN (HEMAGGLUTININ ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36065.457 Da / Num. of mol.: 1 / Fragment: BROMELAIN DIGESTED / Source method: isolated from a natural source Details: A RECOMBINANT INFLUENZA STRAIN CONTAINING A/AICHI/68 (H3N2) HEMAGGLUTININ Source: (natural) Influenza A virus (A/X-31(H3N2)) / Genus: Influenzavirus A / Species: Influenza A virus / Strain: X31 / References: UniProt: P03437, UniProt: P03438*PLUS |
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#2: Protein | Mass: 20212.350 Da / Num. of mol.: 1 / Fragment: BROMELAIN DIGESTED / Source method: isolated from a natural source Details: A RECOMBINANT INFLUENZA STRAIN CONTAINING A/AICHI/68 (H3N2) HEMAGGLUTININ Source: (natural) Influenza A virus (A/X-31(H3N2)) / Genus: Influenzavirus A / Species: Influenza A virus / Strain: X31 / References: UniProt: P03437 |
-Antibody , 2 types, 2 molecules LH
#3: Antibody | Mass: 23980.707 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDROMAS / Strain: BALB/C / References: UniProt: A2NHM3*PLUS |
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#4: Antibody | Mass: 24426.404 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDROMAS / Strain: BALB/C / References: UniProt: P01869*PLUS |
-Sugars , 3 types, 5 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: 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 |
#7: Sugar |
-Non-polymers , 1 types, 70 molecules
#8: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.29 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging dropDetails: Gigant, B., (1995) Proteins: Struct., Funct., Genet., 23, 115. pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 276 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→7 Å / Num. obs: 36133 / % possible obs: 98 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.327 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 159126 |
Reflection shell | *PLUS % possible obs: 95 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→7 Å / Cross valid method: RFREE / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.8→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 7 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.6 |