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Yorodumi- PDB-6ieq: Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ieq | |||||||||
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Title | Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb PGT124 and 35O22 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / HIV-1 / Envelop Protein / Consensus sequence-based ConM SOSIP / broadly neutralizing antibody | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 6alpha-alpha-mannobiose / alpha-D-mannopyranose Function and homology information | |||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å | |||||||||
Authors | Han, B.W. / Wilson, I.A. | |||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence. Authors: Sliepen, K. / Han, B.W. / Bontjer, I. / Mooij, P. / Garces, F. / Behrens, A.J. / Rantalainen, K. / Kumar, S. / Sarkar, A. / Brouwer, P.J.M. / Hua, Y. / Tolazzi, M. / Schermer, E. / Torres, J. ...Authors: Sliepen, K. / Han, B.W. / Bontjer, I. / Mooij, P. / Garces, F. / Behrens, A.J. / Rantalainen, K. / Kumar, S. / Sarkar, A. / Brouwer, P.J.M. / Hua, Y. / Tolazzi, M. / Schermer, E. / Torres, J.L. / Ozorowski, G. / van der Woude, P. / de la Pena, A.T. / van Breemen, M.J. / Camacho-Sanchez, J.M. / Burger, J.A. / Medina-Ramirez, M. / Gonzalez, N. / Alcami, J. / LaBranche, C. / Scarlatti, G. / van Gils, M.J. / Crispin, M. / Montefiori, D.C. / Ward, A.B. / Koopman, G. / Moore, J.P. / Shattock, R.J. / Bogers, W.M. / Wilson, I.A. / Sanders, R.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ieq.cif.gz | 316.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ieq.ent.gz | 253.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ieq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/6ieq ftp://data.pdbj.org/pub/pdb/validation_reports/ie/6ieq | HTTPS FTP |
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-Related structure data
Related structure data | 5cezS 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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2 |
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Unit cell |
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-Components
-Envelope glycoprotein ... , 2 types, 2 molecules GB
#1: Protein | Mass: 56252.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human) |
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#2: Protein | Mass: 17214.486 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human) |
-Antibody , 4 types, 4 molecules LHDE
#3: 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) |
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#4: 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) |
#5: Antibody | Mass: 25783.057 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: 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) |
-Sugars , 8 types, 19 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-(1-3)-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 Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||||||||||
#9: Polysaccharide | Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #10: Polysaccharide | Source method: isolated from a genetically manipulated source #11: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose | #12: 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-(1-6)-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 #13: Sugar | ChemComp-NAG / #14: Sugar | |
-Details
Sequence details | Authors follow residue numbers from HBx numbering, which specifies residue number according to the ...Authors follow residue numbers from HBx numbering, which specifies residue number according to the sequence alignment results with HBx standard. So, those three sequence number gaps come from three short deletions of our ConM SOSIP.v7 sequence. UNK reisues in the sample sequence were just added for the HBx numbering. They are non-entity. |
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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: 4.05 Å3/Da / Density % sol: 69.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.93 Details: 0.07 M sodium acetate, 30% (v/v) glycerol, 6% (w/v) PEG 4000, pH 3.93 PH range: 3.93 - 4.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03315 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03315 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→50 Å / Num. obs: 23583 / % possible obs: 89 % / Redundancy: 17.5 % / CC1/2: 0.95 / Rpim(I) all: 0.04 / Rsym value: 0.15 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 3.9→4.04 Å / Redundancy: 12.3 % / Num. unique obs: 1613 / CC1/2: 0.7 / Rpim(I) all: 0.28 / Rsym value: 1.07 / % possible all: 61.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CEZ Resolution: 3.9→50.01 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: THROUGHOUT / ESU R Free: 0.89 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 247.532 Å2
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Refinement step | Cycle: 1 / Resolution: 3.9→50.01 Å
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Refine LS restraints |
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