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Yorodumi- PDB-6q0e: Inferred precursor (UCA) of the human antibody lineage 652 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q0e | |||||||||
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Title | Inferred precursor (UCA) of the human antibody lineage 652 in complex with influenza hemagglutinin head domain of A/Beijing/262/95(H1N1) | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / 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 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | McCarthy, K.R. / Harrison, S.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Affinity maturation in a human humoral response to influenza hemagglutinin. Authors: McCarthy, K.R. / Raymond, D.D. / Do, K.T. / Schmidt, A.G. / Harrison, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q0e.cif.gz | 369.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q0e.ent.gz | 318.1 KB | Display | PDB format |
PDBx/mmJSON format | 6q0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/6q0e ftp://data.pdbj.org/pub/pdb/validation_reports/q0/6q0e | HTTPS FTP |
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-Related structure data
Related structure data | 6q0hC 6q0iC 6q0lC 6q0oC 6q18C 6q19C 6q1aC 6q1eC 6q1gC 6q1jC 6q1kC C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25338.191 Da / Num. of mol.: 1 / Fragment: Head domain, residues 65-280 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Beijing/262/1995(H1N1)) Strain: A/Beijing/262/1995(H1N1) / Gene: HA / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B4UPF7 |
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-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 22960.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Igl / Cell line (production host): 293F / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 25935.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IgH / Cell line (production host): 293F / Production host: Homo sapiens (human) |
-Non-polymers , 4 types, 340 molecules
#4: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-2PE / |
#6: Chemical | ChemComp-MES / |
#7: Water | ChemComp-HOH / |
-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: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM sodium chloride, 30% (v/v) PEG 400, 100 mM MES |
-Data collection
Diffraction | Mean temperature: 291.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→48.292 Å / Num. obs: 40694 / % possible obs: 99.45 % / Redundancy: 7.05 % / Biso Wilson estimate: 28.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1408 / Net I/σ(I): 13.21 |
Reflection shell | Resolution: 2.15→2.227 Å / Num. unique obs: 4005 / CC1/2: 0.801 / % possible all: 99.78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.292 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.88 Å2 / Biso mean: 39.5336 Å2 / Biso min: 18.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→48.292 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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