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Yorodumi- PDB-3sdy: Crystal Structure of Broadly Neutralizing Antibody CR8020 Bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sdy | ||||||||||||
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Title | Crystal Structure of Broadly Neutralizing Antibody CR8020 Bound to the Influenza A H3 Hemagglutinin | ||||||||||||
Components |
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Keywords | Viral Protein/Immune System / Viral fusion protein / immunoglobulin / Virus attachment and entry / immune recognition / Viral Protein-Immune System complex | ||||||||||||
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 Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||||||||
Authors | Ekiert, D.C. / Wilson, I.A. | ||||||||||||
Citation | Journal: Science / Year: 2011 Title: A highly conserved neutralizing epitope on group 2 influenza A viruses. Authors: Ekiert, D.C. / Friesen, R.H. / Bhabha, G. / Kwaks, T. / Jongeneelen, M. / Yu, W. / Ophorst, C. / Cox, F. / Korse, H.J. / Brandenburg, B. / Vogels, R. / Brakenhoff, J.P. / Kompier, R. / ...Authors: Ekiert, D.C. / Friesen, R.H. / Bhabha, G. / Kwaks, T. / Jongeneelen, M. / Yu, W. / Ophorst, C. / Cox, F. / Korse, H.J. / Brandenburg, B. / Vogels, R. / Brakenhoff, J.P. / Kompier, R. / Koldijk, M.H. / Cornelissen, L.A. / Poon, L.L. / Peiris, M. / Koudstaal, W. / Wilson, I.A. / Goudsmit, J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sdy.cif.gz | 544.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sdy.ent.gz | 475.8 KB | Display | PDB format |
PDBx/mmJSON format | 3sdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/3sdy ftp://data.pdbj.org/pub/pdb/validation_reports/sd/3sdy | HTTPS FTP |
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-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
-Hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 35506.949 Da / Num. of mol.: 1 / Fragment: UNP residues 27-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968(H3N2) / Gene: HA / Plasmid: pFastBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7 |
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#2: Protein | Mass: 20197.312 Da / Num. of mol.: 1 / Fragment: UNP residues 346-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968(H3N2) / Gene: HA / Plasmid: pFastBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7 |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 24344.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin heavy chain locus (IGH) / Cell line (production host): PER.C6 / Production host: Homo sapiens (human) |
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#4: Antibody | Mass: 23581.311 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin kappa chain locus (IGK) / Cell line (production host): PER.C6 / Production host: Homo sapiens (human) |
-Sugars , 5 types, 5 molecules
#5: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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 |
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#6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#7: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 |
#8: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#9: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 1 types, 10 molecules
#10: Chemical | ChemComp-SO4 / |
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-Details
Sequence details | AS PER THE AUTHORS GLY IS THE CORRECT RESIDUE AT THIS POSITION |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 1.8M ammonium sulfate, 100mM sodium acetate 5.4, and 50mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2010 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. all: 60262 / Num. obs: 60239 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 20.4 % / Rsym value: 0.15 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 20.9 % / Rsym value: 0.9969 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→46.61 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 25.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.133 Å2 / ksol: 0.306 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.85→46.61 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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