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Yorodumi- PDB-6mdt: Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and... -
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-Basic information
Entry | Database: PDB / ID: 6mdt | |||||||||
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Title | Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P63 space group | |||||||||
Components |
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Keywords | VIRAL PROTEIN / HIV / ENVELOPE / GLYCOPROTEIN / PREFUSION TRIMER / GLYCAN / HIV-1 GP120 / HIV-1 GP41 / N332 SUPERSITE / IMMUNE SYSTEM / NEUTRALIZING ANTIBODIES / COMPLEX / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX | |||||||||
Function / homology | Function and homology information : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.816 Å | |||||||||
Authors | Kumar, S. / Sarkar, A. / Wilson, I.A. | |||||||||
Citation | Journal: Nat Commun / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mdt.cif.gz | 322.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mdt.ent.gz | 259 KB | Display | PDB format |
PDBx/mmJSON format | 6mdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/6mdt ftp://data.pdbj.org/pub/pdb/validation_reports/md/6mdt | HTTPS FTP |
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-Related structure data
Related structure data | 6mcoC 6me1C 4r26S 5cezS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules BG
#1: Protein | Mass: 17373.867 Da / Num. of mol.: 1 / Fragment: residues 516-668 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: B3UES2 |
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#2: Protein | Mass: 53976.965 Da / Num. of mol.: 1 / Fragment: residues 30-511 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: B3UF58 |
-Antibody , 4 types, 4 molecules DEHL
#3: Antibody | Mass: 26171.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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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.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#5: Antibody | Mass: 25460.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#6: Antibody | Mass: 23056.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Sugars , 8 types, 23 molecules
#7: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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 #8: Polysaccharide | alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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 #9: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #10: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 | Source method: isolated from a genetically manipulated source #12: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 #13: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 #14: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 73.28 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.1M Calcium acetate, 0.1M MES (pH 6), 15%(v/v) PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 28747 / % possible obs: 99.9 % / Redundancy: 10.9 % / CC1/2: 0.77 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 3.8→3.94 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2842 / CC1/2: 0.27 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R26, 5CEZ Resolution: 3.816→41.956 Å / SU ML: 0.8 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.816→41.956 Å
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Refine LS restraints |
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LS refinement shell |
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