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Yorodumi- PDB-5t33: Crystal structure of strain-specific glycan-dependent CD4 binding... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t33 | |||||||||
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Title | Crystal structure of strain-specific glycan-dependent CD4 binding site-directed neutralizing antibody CAP257-RH1, in complex with HIV-1 strain RHPA gp120 core with an oligomannose N276 glycan. | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV / strain-specific / neutralizing antibody / CD4 binding site / N276 glycan / glycan-free V5 | |||||||||
Function / homology | HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2092 Å | |||||||||
Authors | Wibmer, C.K. / Gorman, J. / Kwong, P.D. | |||||||||
Citation | Journal: J.Virol. / Year: 2016 Title: Structure of an N276-Dependent HIV-1 Neutralizing Antibody Targeting a Rare V5 Glycan Hole Adjacent to the CD4 Binding Site. Authors: Wibmer, C.K. / Gorman, J. / Anthony, C.S. / Mkhize, N.N. / Druz, A. / York, T. / Schmidt, S.D. / Labuschagne, P. / Louder, M.K. / Bailer, R.T. / Abdool Karim, S.S. / Mascola, J.R. / ...Authors: Wibmer, C.K. / Gorman, J. / Anthony, C.S. / Mkhize, N.N. / Druz, A. / York, T. / Schmidt, S.D. / Labuschagne, P. / Louder, M.K. / Bailer, R.T. / Abdool Karim, S.S. / Mascola, J.R. / Williamson, C. / Moore, P.L. / Kwong, P.D. / Morris, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t33.cif.gz | 447.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t33.ent.gz | 374.4 KB | Display | PDB format |
PDBx/mmJSON format | 5t33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t33_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5t33_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5t33_validation.xml.gz | 28 KB | Display | |
Data in CIF | 5t33_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/5t33 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/5t33 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules G
#3: Protein | Mass: 39997.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 23888.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Donor CAP257 / Source: (gene. exp.) Homo sapiens (human) / Tissue: Peripheral Blood Mononuclear Cells / Cell: Memory B cell / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 22957.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Donor CAP257 / Source: (gene. exp.) Homo sapiens (human) / Tissue: Peripheral Blood Mononuclear cells / Cell: Memory B cell / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
-Sugars , 4 types, 10 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: 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 #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[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 #7: 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: 2.67 Å3/Da / Density % sol: 53.88 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES (pH7.5) 8% PEG4000 10% Isopropanol 200U/mL Endo H 25% 2-Methyl-2,4-pentanediol as cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 13003 / % possible obs: 81.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 90.23 Å2 / Rmerge(I) obs: 0.102 / Net I/av σ(I): 10.724 / Net I/σ(I): 9.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JZZ, 4HPY, 1NL0 Resolution: 3.2092→47.658 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 249.5 Å2 / Biso mean: 116.9047 Å2 / Biso min: 55.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2092→47.658 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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