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- PDB-3tih: Crystal structure of unliganded HIV-1 clade C strain ZM109F.PB4 g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tih | ||||||
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Title | Crystal structure of unliganded HIV-1 clade C strain ZM109F.PB4 gp120 core | ||||||
![]() | HIV-1 clade C ZM109F.PB4 gp120 | ||||||
![]() | VIRAL PROTEIN / HIV-1 gp120 / unliganded / clade C ZM109F.PB4 | ||||||
Function / homology | HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Beta Complex / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kwon, Y.D. / Kwong, P.D. | ||||||
![]() | ![]() Title: Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops. Authors: Kwon, Y.D. / Finzi, A. / Wu, X. / Dogo-Isonagie, C. / Lee, L.K. / Moore, L.R. / Schmidt, S.D. / Stuckey, J. / Yang, Y. / Zhou, T. / Zhu, J. / Vicic, D.A. / Debnath, A.K. / Shapiro, L. / ...Authors: Kwon, Y.D. / Finzi, A. / Wu, X. / Dogo-Isonagie, C. / Lee, L.K. / Moore, L.R. / Schmidt, S.D. / Stuckey, J. / Yang, Y. / Zhou, T. / Zhu, J. / Vicic, D.A. / Debnath, A.K. / Shapiro, L. / Bewley, C.A. / Mascola, J.R. / Sodroski, J.G. / Kwong, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.6 KB | Display | ![]() |
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PDB format | ![]() | 216.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.1 KB | Display | ![]() |
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Full document | ![]() | 457.5 KB | Display | |
Data in XML | ![]() | 46.2 KB | Display | |
Data in CIF | ![]() | 61.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38547.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 3350, 10% iso-propanol, 0.2 M Ammonium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 14, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4→50 Å / Num. all: 15241 / Num. obs: 12925 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.151 / Rsym value: 0.114 / Net I/σ(I): 6.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 158.036 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 4→46.695 Å
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Refine LS restraints |
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LS refinement shell |
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