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- PDB-7aej: Crystal structure of asymmetric HIV-1 gp41 containing all membran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7aej | ||||||
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Title | Crystal structure of asymmetric HIV-1 gp41 containing all membrane anchors | ||||||
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![]() | VIRAL PROTEIN / membrane fusion | ||||||
Function / homology | ![]() : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caillat, C. / Guilligay, D. / Weissenhorn, W. | ||||||
![]() | ![]() Title: Structure of HIV-1 gp41 with its membrane anchors targeted by neutralizing antibodies. Authors: Caillat, C. / Guilligay, D. / Torralba, J. / Friedrich, N. / Nieva, J.L. / Trkola, A. / Chipot, C.J. / Dehez, F.L. / Weissenhorn, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 267.8 KB | Display | ![]() |
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PDB format | ![]() | 195.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.9 KB | Display | ![]() |
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Full document | ![]() | 461.2 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 26.8 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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Unit cell |
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Components
#1: Protein | Mass: 21824.969 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Gp41 was expressed as two separate chains, one containing residues 512-581 and one containng residues 629-715,Gp41 was expressed as two separate chains, one containing residues 512-581 and ...Details: Gp41 was expressed as two separate chains, one containing residues 512-581 and one containng residues 629-715,Gp41 was expressed as two separate chains, one containing residues 512-581 and one containng residues 629-715,Gp41 was expressed as two separate chains, one containing residues 512-581 and one containng residues 629-715,Gp41 was expressed as two separate chains, one containing residues 512-581 and one containng residues 629-715 Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | | Mass: 13351.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: VHH / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M sodium citrate pH 6.0 0.2M ammonium sulfate 20 % PEG 200 0.1 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→49.56 Å / Num. obs: 11179 / % possible obs: 78.01 % / Redundancy: 9.1 % / Biso Wilson estimate: 85.33 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.23 / Net I/σ(I): 4.75 |
Reflection shell | Resolution: 3.8→3.936 Å / Num. unique obs: 631 / CC1/2: 0.628 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1env, 4b50 Resolution: 3.8→49.56 Å / SU ML: 0.5169 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8736 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→49.56 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 | Refine-ID: X-RAY DIFFRACTION
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