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Yorodumi- PDB-4lss: Crystal structure of broadly and potently neutralizing antibody V... -
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-Basic information
Entry | Database: PDB / ID: 4lss | ||||||
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Title | Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade A strain KER_2018_11 gp120 | ||||||
Components |
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Keywords | viral protein/immune system / antibody antigen complex / Neutralizing antibody VRC01 / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 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 | 4lss.cif.gz | 322.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lss.ent.gz | 263.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/4lss ftp://data.pdbj.org/pub/pdb/validation_reports/ls/4lss | HTTPS FTP |
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-Related structure data
Related structure data | 4lspC 4lsqC 4lsrC 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: 24395.684 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: 23159.688 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, 13 molecules G
#1: Protein | Mass: 39828.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: KER2018_11 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q3ZLH8*PLUS |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 151 molecules
#5: Chemical | #6: Chemical | ChemComp-IPA / | #7: Chemical | #8: 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: 56.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES, 8% PEG 4000, 6.5% isopropanol, pH 7.5, 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 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 3, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: APS ID22 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.59→50 Å / Num. all: 30121 / Num. obs: 27290 / % possible obs: 90.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.127 / Rsym value: 0.098 / Net I/σ(I): 5.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→32.393 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / σ(F): 0 / Phase error: 26.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.861 Å2 / ksol: 0.295 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.59→32.393 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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