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Yorodumi- PDB-5awn: Crystal structure of Human anti-HIV-1 broadly neutralizing antibo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5awn | |||||||||||||||||||||
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Title | Crystal structure of Human anti-HIV-1 broadly neutralizing antibody 3BC176 Fab | |||||||||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 / Env / broadly neutralizing antibody | |||||||||||||||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.887 Å | |||||||||||||||||||||
Authors | Lee, J.H. / Wilson, I.A. / Ward, A.B. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Nat Commun / Year: 2015 Title: Antibodies to a conformational epitope on gp41 neutralize HIV-1 by destabilizing the Env spike. Authors: Jeong Hyun Lee / Daniel P Leaman / Arthur S Kim / Alba Torrents de la Peña / Kwinten Sliepen / Anila Yasmeen / Ronald Derking / Alejandra Ramos / Steven W de Taeye / Gabriel Ozorowski / ...Authors: Jeong Hyun Lee / Daniel P Leaman / Arthur S Kim / Alba Torrents de la Peña / Kwinten Sliepen / Anila Yasmeen / Ronald Derking / Alejandra Ramos / Steven W de Taeye / Gabriel Ozorowski / Florian Klein / Dennis R Burton / Michel C Nussenzweig / Pascal Poignard / John P Moore / Per Johan Klasse / Rogier W Sanders / Michael B Zwick / Ian A Wilson / Andrew B Ward / Abstract: The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. ...The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. By using biochemical, biophysical and computational methods, we map the previously unknown trimer epitopes of two related antibodies, 3BC315 and 3BC176. A cryo-EM reconstruction of a soluble Env trimer bound to 3BC315 Fab at 9.3 Å resolution reveals that the antibody binds between two gp41 protomers, and neutralizes the virus by accelerating trimer decay. In contrast, bnAb 35O22 binding to a partially overlapping quaternary epitope at the gp120-gp41 interface does not induce decay. A conserved gp41-proximal glycan at N88 was also shown to play a role in the binding kinetics of 3BC176 and 3BC315. Finally, our data suggest that the dynamic structure of the Env trimer influences exposure of bnAb epitopes. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5awn.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5awn.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 5awn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5awn_validation.pdf.gz | 431.4 KB | Display | wwPDB validaton report |
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Full document | 5awn_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 5awn_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 5awn_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/5awn ftp://data.pdbj.org/pub/pdb/validation_reports/aw/5awn | HTTPS FTP |
-Related structure data
Related structure data | 3067C 5cckSC 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: 24975.201 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23157.672 Da / Num. of mol.: 1 / Mutation: G108R, N112A, T114S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M sodium citrate pH 5.6, 20% 2-propanol, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Oct 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.887→50 Å / Num. obs: 35026 / % possible obs: 99.7 % / Redundancy: 3.7 % / Net I/σ(I): 16.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CCK Resolution: 1.887→49.894 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.73 / 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: 1.887→49.894 Å
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Refine LS restraints |
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LS refinement shell |
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