+Open data
-Basic information
Entry | Database: PDB / ID: 4hkx | ||||||
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Title | Influenza hemagglutinin in complex with CH67 Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Fab fragment / 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 / 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 / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Schmidt, A.G. / Harrison, S.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody. Authors: Schmidt, A.G. / Xu, H. / Khan, A.R. / O'Donnell, T. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Suphaphiphat, P. / Carfi, A. / Settembre, E.C. / Dormitzer, P.R. / Kepler, T. ...Authors: Schmidt, A.G. / Xu, H. / Khan, A.R. / O'Donnell, T. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Suphaphiphat, P. / Carfi, A. / Settembre, E.C. / Dormitzer, P.R. / Kepler, T.B. / Zhang, R. / Moody, M.A. / Haynes, B.F. / Liao, H.X. / Shaw, D.E. / 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 | 4hkx.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hkx.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hkx_validation.pdf.gz | 460.2 KB | Display | wwPDB validaton report |
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Full document | 4hkx_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 4hkx_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 4hkx_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/4hkx ftp://data.pdbj.org/pub/pdb/validation_reports/hk/4hkx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24890.701 Da / Num. of mol.: 1 / Fragment: UNP residues 65-276 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA1 / Plasmid: pFastBac / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A7UPX0 | ||
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#2: Antibody | Mass: 24903.875 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) | ||
#3: Antibody | Mass: 22800.078 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.17 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 46% PEG400, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2012 |
Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 65129 / Num. obs: 60500 / % possible obs: 91.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 41.26 Å2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.111 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8353 / SU ML: 0.29 / σ(F): 1.37 / Phase error: 23.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.528 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.56 Å2 / Biso mean: 46.5448 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→35.111 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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