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Yorodumi- PDB-5x08: Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E1... -
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-Basic information
Entry | Database: PDB / ID: 5x08 | |||||||||||||||||||||
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Title | Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E10, mutant Npro, with peptide bound | |||||||||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / broadly neutralizing antibody / MPER | |||||||||||||||||||||
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 type 1 | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | |||||||||||||||||||||
Authors | Caaveiro, J.M.M. / Rujas, E. / Nieva, J.L. / Tsumoto, K. | |||||||||||||||||||||
Funding support | Japan, United States, Spain, 6items
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Citation | Journal: J. Mol. Biol. / Year: 2017 Title: Functional Contacts between MPER and the Anti-HIV-1 Broadly Neutralizing Antibody 4E10 Extend into the Core of the Membrane Authors: Rujas, E. / Insausti, S. / Garcia-Porras, M. / Sanchez-Eugenia, R. / Tsumoto, K. / Nieva, J.L. / Caaveiro, J.M.M. #1: Journal: J. Virol. / Year: 2015 Title: Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10. Authors: Rujas, E. / Gulzar, N. / Morante, K. / Tsumoto, K. / Scott, J.K. / Nieva, J.L. / Caaveiro, J.M.M. #2: Journal: J. Virol. / Year: 2016 Title: Reply to "The Broadly Neutralizing, Anti-HIV Antibody 4E10: an Open and Shut Case?". Authors: Rujas, E. / Gulzar, N. / Morante, K. / Tsumoto, K. / Scott, J.K. / Nieva, J.L. / Caaveiro, J.M.M. #3: 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.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 | 5x08.cif.gz | 211.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x08.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 5x08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x08_validation.pdf.gz | 688.4 KB | Display | wwPDB validaton report |
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Full document | 5x08_full_validation.pdf.gz | 689 KB | Display | |
Data in XML | 5x08_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 5x08_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/5x08 ftp://data.pdbj.org/pub/pdb/validation_reports/x0/5x08 | HTTPS FTP |
-Related structure data
Related structure data | 4wy7S 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 on special symmetry positions |
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-Components
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 2187.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (MAL ISOLATE) Gene: ENV / Production host: synthetic construct (others) / References: UniProt: P04578*PLUS |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24184.256 Da / Num. of mol.: 1 / Mutation: Insertion Pro-Pro at position 99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IgG1 / Plasmid: pColaDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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) / Gene: IgG1 / Plasmid: pColaDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): T7 SHUFFLE |
-Non-polymers , 6 types, 487 molecules
#4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-P6G / | #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-ACT / | #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: 2.75 Å3/Da / Density % sol: 55.28 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100mM sodium acetate; 34% PEG4000; 225mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979133 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979133 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→22.25 Å / Num. obs: 88101 / % possible obs: 99.5 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.035 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.49→1.57 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 12788 / CC1/2: 0.666 / Rpim(I) all: 0.344 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WY7 Resolution: 1.49→22.25 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.333 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.179 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→22.25 Å
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Refine LS restraints |
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