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- PDB-6me1: Crystal structure of the clade B isolate B41 mutant fusion peptid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6me1 | ||||||
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Title | Crystal structure of the clade B isolate B41 mutant fusion peptide (residues 512-521) in complex with VRC34.01 | ||||||
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![]() | VIRAL PROTEIN / HIV / ENVELOPE / FUSION PEPTIDE / HIV-1 GP41 / IMMUNE SYSTEM / NEUTRALIZING ANTIBODIES / COMPLEX / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | ![]() host cell periphery / CD4 receptor binding / Dectin-2 family / 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 / host cell perinuclear region of cytoplasm / viral protein processing ...host cell periphery / CD4 receptor binding / Dectin-2 family / 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 / host cell perinuclear region of cytoplasm / 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 / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, S. / Sarkar, A. / Wilson, I.A. | ||||||
![]() | ![]() Title: Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide. Authors: Kumar, S. / Sarkar, A. / Pugach, P. / Sanders, R.W. / Moore, J.P. / Ward, A.B. / Wilson, I.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.2 KB | Display | ![]() |
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PDB format | ![]() | 152.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.5 KB | Display | ![]() |
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Full document | ![]() | 473.9 KB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 54.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mcoC ![]() 6mdtC ![]() 5i8cS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23797.615 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23138.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein/peptide | Mass: 1731.958 Da / Num. of mol.: 2 / Fragment: residues 512-521 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium sulfate, 20%(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 72903 / % possible obs: 99.3 % / Redundancy: 3.2 % / CC1/2: 0.89 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.97→2.01 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3639 / CC1/2: 0.64 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5I8C Resolution: 1.97→38.18 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→38.18 Å
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Refine LS restraints |
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LS refinement shell |
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