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- PDB-6ce0: Crystal structure of a HIV-1 clade B tier-3 isolate H078.14 UFO-B... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ce0 | |||||||||
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Title | Crystal structure of a HIV-1 clade B tier-3 isolate H078.14 UFO-BG Env trimer in complex with broadly neutralizing Fabs PGT124 and 35O22 at 4.6 Angstrom | |||||||||
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![]() | viral protein/immune system / HIV-1 gp140 / Uncleaved prefusion-optimized (UFO) / immune system / viral-protein complex / viral envelope trimer / broadly neutralizing antibody / VIRAL PROTEIN / viral protein-immune system complex | |||||||||
Function / homology | ![]() virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / viral process / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing ...virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / viral process / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 | ![]() ![]() ![]() | |||||||||
![]() | Kumar, S. / Sarkar, A. / Wilson, I.A. | |||||||||
![]() | ![]() Title: HIV-1 vaccine design through minimizing envelope metastability. Authors: He, L. / Kumar, S. / Allen, J.D. / Huang, D. / Lin, X. / Mann, C.J. / Saye-Francisco, K.L. / Copps, J. / Sarkar, A. / Blizard, G.S. / Ozorowski, G. / Sok, D. / Crispin, M. / Ward, A.B. / ...Authors: He, L. / Kumar, S. / Allen, J.D. / Huang, D. / Lin, X. / Mann, C.J. / Saye-Francisco, K.L. / Copps, J. / Sarkar, A. / Blizard, G.S. / Ozorowski, G. / Sok, D. / Crispin, M. / Ward, A.B. / Nemazee, D. / Burton, D.R. / Wilson, I.A. / Zhu, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 316.9 KB | Display | ![]() |
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PDB format | ![]() | 253 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 56.1 KB | Display | |
Data in CIF | ![]() | 74.5 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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Unit cell |
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Components
-Envelope glycoprotein ... , 2 types, 2 molecules BG
#1: Protein | Mass: 15702.743 Da / Num. of mol.: 1 / Mutation: T602C,T602C,T602C,T602C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 54100.199 Da / Num. of mol.: 1 / Mutation: C500A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein , 1 types, 1 molecules H
#5: Protein | Mass: 25460.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Antibody , 3 types, 3 molecules DEL
#3: Antibody | Mass: 26171.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#4: Antibody | Mass: 23318.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#6: Antibody | Mass: 23056.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 6 types, 22 molecules ![](data/chem/img/NAG.gif)
#7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #11: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #12: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.43 Å3/Da / Density % sol: 72.2 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.1 Tris (pH 7.4), 0.2 M lithium sulfate, 6% (w/v) polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 4.6→50 Å / Num. obs: 15619 / % possible obs: 96.9 % / Redundancy: 5.3 % / CC1/2: 0.76 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 4.6→4.68 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.25 / Num. unique obs: 798 / CC1/2: 0.58 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4R26, 5CEZ Resolution: 4.602→48.866 Å / SU ML: 0.94 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.602→48.866 Å
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Refine LS restraints |
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LS refinement shell |
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