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Yorodumi- PDB-7jix: Murine antibody that engages the influenza hemagglutinin receptor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jix | ||||||
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Title | Murine antibody that engages the influenza hemagglutinin receptor binding site | ||||||
Components |
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Keywords | Viral protein/IMMUNE SYSTEM / antibody / influenza / hemagglutinin / IMMUNE SYSTEM / Viral protein-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical 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 Similarity search - Function | ||||||
Biological species | Influenza A virus Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.901 Å | ||||||
Authors | Bajic, G. / Schmidt, A.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Murine antibody that engages the influenza hemagglutinin receptor binding site Authors: Bajic, G. / Schmidt, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jix.cif.gz | 200.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jix.ent.gz | 156.5 KB | Display | PDB format |
PDBx/mmJSON format | 7jix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/7jix ftp://data.pdbj.org/pub/pdb/validation_reports/ji/7jix | HTTPS FTP |
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-Related structure data
Related structure data | 5ugyS S: Starting model for refinement |
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Similar structure data |
-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: 37239.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006 (Egg passage)(H1N1)) Strain: A/Solomon Islands/3/2006 (Egg passage)(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8A6 |
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#2: Protein | Mass: 20269.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Mexico/UASLP-006/2008(H1N1)) Strain: A/Mexico/UASLP-006/2008(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G2TTT7 |
-Antibody , 2 types, 2 molecules LH
#3: Antibody | Mass: 24086.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
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#4: Antibody | Mass: 24222.092 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
-Sugars , 2 types, 3 molecules
#5: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-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 |
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#6: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Details
Has ligand of interest | N |
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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: 6.16 Å3/Da / Density % sol: 80.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 400, CHES pH 9.0, 100mM MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999935 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999935 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→48.15 Å / Num. obs: 25174 / % possible obs: 97.65 % / Redundancy: 1.1 % / CC1/2: 1 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3.901→4.04 Å / Num. unique obs: 2324 / CC1/2: 1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UGY Resolution: 3.901→48.15 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 259.36 Å2 / Biso mean: 91.99 Å2 / Biso min: 22.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.901→48.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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