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Yorodumi- PDB-4r26: Crystal structure of human Fab PGT124, a broadly neutralizing and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r26 | ||||||
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Title | Crystal structure of human Fab PGT124, a broadly neutralizing and potent HIV-1 neutralizing antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IGG Fold / Antibody / HIV-1 binding | ||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / adaptive immune response / Potential therapeutics for SARS / blood microparticle / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Nomascus leucogenys (northern white-cheeked gibbon) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4969 Å | ||||||
Authors | Garces, F. / Kong, L. / Wilson, I.A. | ||||||
Citation | Journal: Cell / Year: 2014 Title: Structural evolution of glycan recognition by a family of potent HIV antibodies. Authors: Fernando Garces / Devin Sok / Leopold Kong / Ryan McBride / Helen J Kim / Karen F Saye-Francisco / Jean-Philippe Julien / Yuanzi Hua / Albert Cupo / John P Moore / James C Paulson / Andrew B ...Authors: Fernando Garces / Devin Sok / Leopold Kong / Ryan McBride / Helen J Kim / Karen F Saye-Francisco / Jean-Philippe Julien / Yuanzi Hua / Albert Cupo / John P Moore / James C Paulson / Andrew B Ward / Dennis R Burton / Ian A Wilson / Abstract: The HIV envelope glycoprotein (Env) is densely covered with self-glycans that should help shield it from recognition by the human immune system. Here, we examine how a particularly potent family of ...The HIV envelope glycoprotein (Env) is densely covered with self-glycans that should help shield it from recognition by the human immune system. Here, we examine how a particularly potent family of broadly neutralizing antibodies (Abs) has evolved common and distinct structural features to counter the glycan shield and interact with both glycan and protein components of HIV Env. The inferred germline antibody already harbors potential binding pockets for a glycan and a short protein segment. Affinity maturation then leads to divergent evolutionary branches that either focus on a single glycan and protein segment (e.g., Ab PGT124) or engage multiple glycans (e.g., Abs PGT121-123). Furthermore, other surrounding glycans are avoided by selecting an appropriate initial antibody shape that prevents steric hindrance. Such molecular recognition lessons are important for engineering proteins that can recognize or accommodate glycans. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r26.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r26.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 4r26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r26_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 4r26_full_validation.pdf.gz | 477.1 KB | Display | |
Data in XML | 4r26_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4r26_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/4r26 ftp://data.pdbj.org/pub/pdb/validation_reports/r2/4r26 | 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
#1: Antibody | Mass: 23056.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nomascus leucogenys (northern white-cheeked gibbon), (gene. exp.) Homo sapiens (human) Gene: IGLC3 / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P0DOY3, UniProt: S6BGD6*PLUS | ||
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#2: Antibody | Mass: 25460.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P0DOX5, UniProt: Q6GMX6*PLUS | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 4000, 0.2M MgCl2, 0.1M Tris-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.4969→42.211 Å / Num. all: 15032 / Num. obs: 14303 / % possible obs: 95.4 % / Observed criterion σ(F): 2.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4969→42.211 Å / SU ML: 0.31 / Phase error: 31.27 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4969→42.211 Å
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Refine LS restraints |
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LS refinement shell |
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