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- PDB-4yc2: Crystal structure of the stabilized inner domain of clade A/E HIV... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yc2 | ||||||
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Title | Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 from E. coli in complex with the antibody A32. | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / ADCC / NON-NEUTRALIZING / ANTI-HIV-1 ENV ANTIBODY A32 / CD4I ANTIBODY / CLADE A/E 93TH057 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / viral envelope / Immunoglobulin-like / Sandwich / Mainly Beta / clade A/E 93TH057 HIV-1 gp120 core![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tolbert, W.D. / Gohain, N. / Pazgier, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Paring Down HIV Env: Design and Crystal Structure of a Stabilized Inner Domain of HIV-1 gp120 Displaying a Major ADCC Target of the A32 Region. Authors: Tolbert, W.D. / Gohain, N. / Veillette, M. / Chapleau, J.P. / Orlandi, C. / Visciano, M.L. / Ebadi, M. / DeVico, A.L. / Fouts, T.R. / Finzi, A. / Lewis, G.K. / Pazgier, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 439 KB | Display | ![]() |
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PDB format | ![]() | 363.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.4 KB | Display | ![]() |
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Full document | ![]() | 495.3 KB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yblC ![]() 5fcuC ![]() 3tnmS ![]() 4rqh S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | Complexes were purified by gel filtration prior to crystallization |
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Components
#1: Protein | Mass: 17380.535 Da / Num. of mol.: 2 / Mutation: V65C, S115C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 23991.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 22193.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Water | ChemComp-HOH / | Sequence details | The sequence of the clade A/E gp120 is based on the HIV-1 clade A/E gp120 sequence in PDB ID 3TGT. ...The sequence of the clade A/E gp120 is based on the HIV-1 clade A/E gp120 sequence in PDB ID 3TGT. The sequence was engineered to remove the outer domain of gp120 and consists of the N-terminal sequence plus some of the C-terminal sequence. The numbering in the PDB file is consistent with 3TGT and 4H8W and is based on the Hxbc2 gp120 sequence which serves as the reference sequence for most gp120 structures. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 18-22% PEG 6000 or PEG8000 0.1 M Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 23714 / Num. obs: 20655 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / % possible all: 86.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TNM and 4RQH Resolution: 3.02→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.888 / SU B: 72.5 / SU ML: 0.556 / Cross valid method: THROUGHOUT / ESU R Free: 0.616 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.657 Å2
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Refinement step | Cycle: 1 / Resolution: 3.02→50 Å
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Refine LS restraints |
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