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Yorodumi- PDB-5wdf: Crystal structure of 10E8v4-5R+100cF Fab in complex with HIV-1 gp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wdf | ||||||
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Title | Crystal structure of 10E8v4-5R+100cF Fab in complex with HIV-1 gp41 peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 neutralizing antibody / MPER / 10E8 | ||||||
Function / homology | Function and homology information Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Kwon, Y.D. / Kwong, P.D. | ||||||
Citation | Journal: Cell Rep / Year: 2018 Title: Surface-Matrix Screening Identifies Semi-specific Interactions that Improve Potency of a Near Pan-reactive HIV-1-Neutralizing Antibody. Authors: Kwon, Y.D. / Chuang, G.Y. / Zhang, B. / Bailer, R.T. / Doria-Rose, N.A. / Gindin, T.S. / Lin, B. / Louder, M.K. / McKee, K. / O'Dell, S. / Pegu, A. / Schmidt, S.D. / Asokan, M. / Chen, X. / ...Authors: Kwon, Y.D. / Chuang, G.Y. / Zhang, B. / Bailer, R.T. / Doria-Rose, N.A. / Gindin, T.S. / Lin, B. / Louder, M.K. / McKee, K. / O'Dell, S. / Pegu, A. / Schmidt, S.D. / Asokan, M. / Chen, X. / Choe, M. / Georgiev, I.S. / Jin, V. / Pancera, M. / Rawi, R. / Wang, K. / Chaudhuri, R. / Kueltzo, L.A. / Manceva, S.D. / Todd, J.P. / Scorpio, D.G. / Kim, M. / Reinherz, E.L. / Wagh, K. / Korber, B.M. / Connors, M. / Shapiro, L. / Mascola, J.R. / Kwong, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wdf.cif.gz | 348.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wdf.ent.gz | 287 KB | Display | PDB format |
PDBx/mmJSON format | 5wdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wdf_validation.pdf.gz | 467.4 KB | Display | wwPDB validaton report |
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Full document | 5wdf_full_validation.pdf.gz | 478.7 KB | Display | |
Data in XML | 5wdf_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 5wdf_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/5wdf ftp://data.pdbj.org/pub/pdb/validation_reports/wd/5wdf | HTTPS FTP |
-Related structure data
Related structure data | 5iq9S 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
#1: Antibody | Mass: 25169.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: 1GHG1 / Plasmid: pVRC8400 / Cell line (production host): Expi 293S / Production host: Homo sapiens (human) #2: Antibody | Mass: 22879.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGLC2 / Plasmid: pVRC8400 / Cell line (production host): Expi 293S / Production host: Homo sapiens (human) #3: Protein/peptide | Mass: 2330.745 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS |
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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: 2.18 Å3/Da / Density % sol: 43.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG3350, 10% iso-propanol, 0.1M Ammonium citrate, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 18005 / % possible obs: 93.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 11 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.1 / % possible all: 83.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5iq9 Resolution: 3.1→45.121 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 32.91 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→45.121 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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