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Yorodumi- PDB-4wy7: Crystal structure of recombinant 4E10 expressed in Escherichia co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wy7 | ||||||
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Title | Crystal structure of recombinant 4E10 expressed in Escherichia coli with epitope bound | ||||||
Components |
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Keywords | IMMUNE SYSTEM / broad neutralizing antobody / recombinant Fab / epitope | ||||||
Function / homology | Function and homology information Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / structural molecule activity / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus type 1 group M subtype B | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rujas, E. / Morante, K. / Tsumoto, K. / Nieva, J.L. / Caaveiro, J.M.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region. Authors: Apellaniz, B. / Rujas, E. / Serrano, S. / Morante, K. / Tsumoto, K. / Caaveiro, J.M. / Jimenez, M.A. / Nieva, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wy7.cif.gz | 108.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wy7.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 4wy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/4wy7 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/4wy7 | HTTPS FTP |
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-Related structure data
Related structure data | 2mg1C 2mg2C 2mg3C 2fx7S S: Starting model for refinement 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
#1: Antibody | Mass: 23990.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle | ||
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#2: Antibody | Mass: 23292.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle | ||
#3: Protein/peptide | Mass: 2187.582 Da / Num. of mol.: 1 / Fragment: UNP residues 662-674 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B Strain: isolate WMJ22 / Gene: env / Production host: synthetic construct (others) / References: UniProt: P05880 | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.58 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 200 mM sodium acetate 30% PEG 8,000 100 mM sodium cacodylate Protein was prepared in PBS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→44.7 Å / Num. obs: 30114 / % possible obs: 94.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.3 / % possible all: 76.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FX7 Resolution: 2.1→44.7 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.171 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.78 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→44.7 Å
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Refine LS restraints |
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