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Yorodumi- PDB-6muf: Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6muf | |||||||||
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Title | Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.4 Angstrom | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/INHIBITOR / HIV-1 Envelope Prefusion Trimer / Entry Inhibitors / IMMUNE SYSTEM-INHIBITOR 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 / viral envelope ...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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.91 Å | |||||||||
Authors | Lai, Y.-T. / Kwong, P.D. | |||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry. Authors: Lai, Y.T. / Wang, T. / O'Dell, S. / Louder, M.K. / Schon, A. / Cheung, C.S.F. / Chuang, G.Y. / Druz, A. / Lin, B. / McKee, K. / Peng, D. / Yang, Y. / Zhang, B. / Herschhorn, A. / Sodroski, J. ...Authors: Lai, Y.T. / Wang, T. / O'Dell, S. / Louder, M.K. / Schon, A. / Cheung, C.S.F. / Chuang, G.Y. / Druz, A. / Lin, B. / McKee, K. / Peng, D. / Yang, Y. / Zhang, B. / Herschhorn, A. / Sodroski, J. / Bailer, R.T. / Doria-Rose, N.A. / Mascola, J.R. / Langley, D.R. / Kwong, P.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6muf.cif.gz | 262.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6muf.ent.gz | 210.9 KB | Display | PDB format |
PDBx/mmJSON format | 6muf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/6muf ftp://data.pdbj.org/pub/pdb/validation_reports/mu/6muf | HTTPS FTP |
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-Related structure data
Related structure data | 6mtjC 6mtnC 6mu6C 6mu7C 6mu8C 6mugC C: citing same article (ref.) |
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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
-Envelope glycoprotein ... , 2 types, 2 molecules BG
#1: Protein | Mass: 17357.824 Da / Num. of mol.: 1 / Fragment: gp41 / Mutation: I559P, A605C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: B3UEZ6 |
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#4: Protein | Mass: 54991.215 Da / Num. of mol.: 1 / Fragment: gp120 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 |
-Antibody , 4 types, 4 molecules DEHL
#2: Antibody | Mass: 14662.336 Da / Num. of mol.: 1 / Mutation: E10T, L11T, K12T, A16S, I68N, K83T, F84S, Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 12358.635 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: 26255.498 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: 23416.145 Da / Num. of mol.: 1 / Mutation: E184M, S188M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Sugars , 5 types, 15 molecules
#7: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-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 |
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#8: 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 |
#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 | 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-(1-2)-alpha-D-mannopyranose-(1-6)-[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 |
#11: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.31 Å3/Da / Density % sol: 76.83 % |
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Crystal grow | Temperature: 298 K / Method: evaporation Details: 90mM Na Acetate pH5.5 6% PEG8,000 3% PEG400 450mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 5, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 29704 / % possible obs: 43.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.22 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.041 / Rrim(I) all: 0.087 / Χ2: 0.777 / Net I/σ(I): 6.9 / Num. measured all: 96862 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2.91→41.836 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 29.44 / Stereochemistry target values: ML
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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 max: 168.69 Å2 / Biso mean: 51.1955 Å2 / Biso min: 1.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.91→41.836 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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