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Yorodumi- PDB-6fy0: Crystal structure of a V2-directed, RV144 vaccine-like antibody f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fy0 | ||||||
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Title | Crystal structure of a V2-directed, RV144 vaccine-like antibody from HIV-1 infection, CAP228-16H, bound to a heterologous V2 peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / HIV V2 peptide | ||||||
Function / homology | Function and homology information virus-mediated perturbation of host defense response => GO:0019049 / : / 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 / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane ...virus-mediated perturbation of host defense response => GO:0019049 / : / 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 / membrane => GO:0016020 / 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 / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Wibmer, C.K. / Fernandes, M. / Vijayakumar, B. / Dirr, H.W. / Sayed, Y. / Moore, P.L. / Morris, L. | ||||||
Citation | Journal: Cell Rep / Year: 2018 Title: V2-Directed Vaccine-like Antibodies from HIV-1 Infection Identify an Additional K169-Binding Light Chain Motif with Broad ADCC Activity. Authors: van Eeden, C. / Wibmer, C.K. / Scheepers, C. / Richardson, S.I. / Nonyane, M. / Lambson, B. / Mkhize, N.N. / Vijayakumar, B. / Sheng, Z. / Stanfield-Oakley, S. / Bhiman, J.N. / Bekker, V. / ...Authors: van Eeden, C. / Wibmer, C.K. / Scheepers, C. / Richardson, S.I. / Nonyane, M. / Lambson, B. / Mkhize, N.N. / Vijayakumar, B. / Sheng, Z. / Stanfield-Oakley, S. / Bhiman, J.N. / Bekker, V. / Hermanus, T. / Mabvakure, B. / Ismail, A. / Moody, M.A. / Wiehe, K. / Garrett, N. / Karim, S.A. / Dirr, H. / Fernandes, M.A. / Sayed, Y. / Shapiro, L. / Ferrari, G. / Haynes, B.F. / Moore, P.L. / Morris, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fy0.cif.gz | 496.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fy0.ent.gz | 419 KB | Display | PDB format |
PDBx/mmJSON format | 6fy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fy0_validation.pdf.gz | 468.6 KB | Display | wwPDB validaton report |
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Full document | 6fy0_full_validation.pdf.gz | 476.7 KB | Display | |
Data in XML | 6fy0_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 6fy0_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/6fy0 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/6fy0 | HTTPS FTP |
-Related structure data
Related structure data | 4hqqS 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
#1: Antibody | Mass: 25145.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Donor CAP228 / Source: (gene. exp.) Homo sapiens (human) / Cell: Memory B cell / Cell line (production host): FreeStyle 293-F Cells / Production host: Homo sapiens (human) #2: Antibody | Mass: 22647.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Donor CAP228 / Source: (gene. exp.) Homo sapiens (human) / Cell: Memory B cell / Cell line (production host): FreeStyle 293-F Cells / Production host: Homo sapiens (human) #3: Protein/peptide | Mass: 2344.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: synthetic construct (others) / References: UniProt: L7TQU8*PLUS #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.22 Å3/Da / Density % sol: 44.67 % / Description: Large diamond shaped crystals (0.3-0.5mm) |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 20% PEG8000, 200mM sodium chloride, 100mM sodium phosphate-citrate (pH4.2), 160mM ammonium sulphate, 8% 2-Methyl-2,4-pentanediol (25% 2-Methyl-2,4-pentanediol for cryoprotection) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 28958 / % possible obs: 91.3 % / Redundancy: 5.1 % / CC1/2: 0.987 / Rpim(I) all: 0.068 / Rsym value: 0.158 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1701 / CC1/2: 0.873 / Rpim(I) all: 0.263 / Rsym value: 0.373 / % possible all: 60.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HQQ Resolution: 2.57→50 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.57→50 Å
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