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Yorodumi- PDB-4lsq: Crystal structure of broadly and potently neutralizing antibody V... -
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-Basic information
Entry | Database: PDB / ID: 4lsq | ||||||
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Title | Crystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E gp120 93TH057 with LOOP D and Loop V5 from clade A strain 3415_v1_c1 | ||||||
Components |
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Keywords | viral protein/immune system / Neutralizing antibody VRC-CH31 / viral protein-immune system complex | ||||||
Function / homology | Function and homology information 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 ...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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å | ||||||
Authors | Zhou, T. / Moquin, S. / Kwong, P.D. | ||||||
Citation | Journal: Immunity / Year: 2013 Title: Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies. Authors: Zhou, T. / Zhu, J. / Wu, X. / Moquin, S. / Zhang, B. / Acharya, P. / Georgiev, I.S. / Altae-Tran, H.R. / Chuang, G.Y. / Joyce, M.G. / Do Kwon, Y. / Longo, N.S. / Louder, M.K. / Luongo, T. / ...Authors: Zhou, T. / Zhu, J. / Wu, X. / Moquin, S. / Zhang, B. / Acharya, P. / Georgiev, I.S. / Altae-Tran, H.R. / Chuang, G.Y. / Joyce, M.G. / Do Kwon, Y. / Longo, N.S. / Louder, M.K. / Luongo, T. / McKee, K. / Schramm, C.A. / Skinner, J. / Yang, Y. / Yang, Z. / Zhang, Z. / Zheng, A. / Bonsignori, M. / Haynes, B.F. / Scheid, J.F. / Nussenzweig, M.C. / Simek, M. / Burton, D.R. / Koff, W.C. / Mullikin, J.C. / Connors, M. / Shapiro, L. / Nabel, G.J. / 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 | 4lsq.cif.gz | 452.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lsq.ent.gz | 380.2 KB | Display | PDB format |
PDBx/mmJSON format | 4lsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/4lsq ftp://data.pdbj.org/pub/pdb/validation_reports/ls/4lsq | HTTPS FTP |
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-Related structure data
Related structure data | 4lspC 4lsrC 4lssC 4lstC 4lsuC 4lsvC 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
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 25571.658 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 22854.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) |
-Protein / Sugars , 2 types, 10 molecules G
#1: Protein | Mass: 39182.434 Da / Num. of mol.: 1 / Mutation: N70D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: 93TH057 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 395 molecules
#5: Chemical | ChemComp-CD / #6: Chemical | ChemComp-BU3 / ( | #7: Chemical | #8: Chemical | ChemComp-NA / #9: Water | ChemComp-HOH / | |
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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: 2.84 Å3/Da / Density % sol: 56.65 % |
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Crystal grow | Temperature: 293 K / pH: 8.5 Details: 0.1M Tris, 8.25% PEG 8000, 0.02 M CdCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 18, 2011 |
Radiation | Monochromator: APS 22ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 47596 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 39.25 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.522 / % possible all: 87.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→49.38 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.63 / σ(F): 1.35 / Phase error: 23.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.72 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→49.38 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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