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Yorodumi- PDB-6ch9: Crystal structure of a natively-glycosylated B41 SOSIP.664 HIV-1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ch9 | ||||||||||||
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Title | Crystal structure of a natively-glycosylated B41 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and 35O22 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Env glycoprotein / broadly neutralizing antibodies | ||||||||||||
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 / 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 ...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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.85 Å | ||||||||||||
Authors | Barnes, C.O. / Bjorkman, P.J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural characterization of a highly-potent V3-glycan broadly neutralizing antibody bound to natively-glycosylated HIV-1 envelope. Authors: Barnes, C.O. / Gristick, H.B. / Freund, N.T. / Escolano, A. / Lyubimov, A.Y. / Hartweger, H. / West, A.P. / Cohen, A.E. / Nussenzweig, M.C. / Bjorkman, P.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ch9.cif.gz | 289.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ch9.ent.gz | 228.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ch9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ch9_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 6ch9_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 6ch9_validation.xml.gz | 61.7 KB | Display | |
Data in CIF | 6ch9_validation.cif.gz | 81.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/6ch9 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/6ch9 | HTTPS FTP |
-Related structure data
Related structure data | 6ch7C 6ch8C 6chbC 4toyS 5t3zS 5ud9S S: Starting model for refinement 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pAM/C / Cell line (production host): K1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: B3UEZ6 |
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#4: Protein | Mass: 57929.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pAM/C / Cell line (production host): K1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: B3UES2 |
-Protein , 2 types, 2 molecules DQ
#2: Protein | Mass: 26171.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) |
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#5: Protein | Mass: 26020.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Antibody , 2 types, 2 molecules ER
#3: Antibody | Mass: 23318.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) |
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#6: Antibody | Mass: 23021.447 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, 19 molecules
#7: 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 #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 | Source method: isolated from a genetically manipulated source #10: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...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 #11: 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 #12: 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 #13: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...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 #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: 5.54 Å3/Da / Density % sol: 77.81 % / Mosaicity: 0.19 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 5% Tacismate pH 8.0, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.85→39.9 Å / Num. obs: 18521 / % possible obs: 99.8 % / Redundancy: 9.9 % / Biso Wilson estimate: 283.59 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.086 / Rrim(I) all: 0.273 / Net I/σ(I): 5 / Num. measured all: 183962 / Scaling rejects: 310 |
Reflection shell | Resolution: 4.85→5.31 Å / Redundancy: 9.6 % / Rmerge(I) obs: 5.063 / Num. unique obs: 4397 / CC1/2: 0.347 / Rpim(I) all: 1.712 / Rrim(I) all: 5.351 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T3Z, 5UD9, 4TOY Resolution: 4.85→39.9 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.146
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Displacement parameters | Biso mean: 281.83 Å2
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Refine analyze | Luzzati coordinate error obs: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 4.85→39.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.85→5.14 Å / Total num. of bins used: 9
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