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Yorodumi- PDB-4r2g: Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core a... -
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Basic information
| Entry | Database: PDB / ID: 4r2g | ||||||||||||
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| Title | Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4 | ||||||||||||
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Keywords | IMMUNE SYSTEM / Protein-Protein complex / IgG / Anti-HIV antibodies / gp120 | ||||||||||||
| Function / homology | Function and homology informationhelper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / cellular response to ionomycin / maintenance of protein location in cell / response to methamphetamine hydrochloride / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / cellular response to ionomycin / maintenance of protein location in cell / response to methamphetamine hydrochloride / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / CD22 mediated BCR regulation / regulation of T cell activation / positive regulation of monocyte differentiation / response to vitamin D / IgG immunoglobulin complex / Alpha-defensins / Nef Mediated CD4 Down-regulation / Fc epsilon receptor (FCERI) signaling / leukocyte chemotaxis / Other interleukin signaling / Classical antibody-mediated complement activation / T cell receptor complex / immunoglobulin mediated immune response / extracellular matrix structural constituent / enzyme-linked receptor protein signaling pathway / Dectin-2 family / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / macrophage differentiation / positive regulation of calcium ion transport into cytosol / Generation of second messenger molecules / FCGR activation / T cell differentiation / immunoglobulin binding / Co-inhibition by PD-1 / Role of LAT2/NTAL/LAB on calcium mobilization / Binding and entry of HIV virion / Role of phospholipids in phagocytosis / immunoglobulin complex / Scavenging of heme from plasma / antigen binding / coreceptor activity / positive regulation of plasma membrane raft polarization / positive regulation of interleukin-2 production / positive regulation of receptor clustering / symbiont-mediated perturbation of host defense response / positive regulation of T cell proliferation / FCERI mediated Ca+2 mobilization / B cell receptor signaling pathway / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / Regulation of Complement cascade / protein tyrosine kinase binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / host cell endosome membrane / Cell surface interactions at the vascular wall / T cell activation / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / clathrin-coated endocytic vesicle membrane / Vpu mediated degradation of CD4 / Regulation of actin dynamics for phagocytic cup formation / T cell receptor signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / FCERI mediated NF-kB activation / positive regulation of inflammatory response / response to estradiol / MHC class II protein complex binding / transmembrane signaling receptor activity / Downstream TCR signaling / positive regulation of cell growth / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / blood microparticle / clathrin-dependent endocytosis of virus by host cell / Potential therapeutics for SARS / response to ethanol / Initial triggering of complement / adaptive immune response / early endosome / cell surface receptor signaling pathway / cell adhesion / viral protein processing / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host plasma membrane / signaling receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / lipid binding / protein kinase binding / endoplasmic reticulum membrane / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | ||||||||||||
| Biological species | Human immunodeficiency virus type 1 group M subtype B Homo sapiens (human) | ||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.283 Å | ||||||||||||
Authors | Garces, F. / Wilson, I.A. | ||||||||||||
Citation | Journal: Cell / Year: 2014Title: 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. | ||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4r2g.cif.gz | 724.6 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4r2g.ent.gz | 601.3 KB | Display | PDB format |
| PDBx/mmJSON format | 4r2g.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/4r2g ftp://data.pdbj.org/pub/pdb/validation_reports/r2/4r2g | HTTPS FTP |
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-Related structure data
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 3 | ![]()
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| 4 | ![]()
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| Unit cell |
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Components
-Protein , 2 types, 8 molecules EOAKFBHL
| #1: Protein | Mass: 34754.543 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype BStrain: isolate JRCSF / Gene: env / Cell line (production host): 293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: P20871#2: Protein | Mass: 20419.252 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: ![]() |
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-Antibody , 2 types, 8 molecules PCIMQDJN
| #3: Antibody | Mass: 23056.605 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@, IGLC3 / Cell line (production host): 293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: P0DOY3#4: Antibody | Mass: 25460.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Cell line (production host): 293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: P0DOX5 |
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-Sugars , 3 types, 32 molecules 
| #5: 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-(1-2)-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 #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 8 molecules 


| #8: Chemical | ChemComp-CL / #9: Chemical | ChemComp-GOL / |
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-Details
| Has protein modification | Y |
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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: 3.77 Å3/Da / Density % sol: 67.34 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.4M ammonium sulphate, 0.1M Tris, 13% glycerol, pH 8.0, 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: 1 Å |
| Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2013 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
| Reflection | Resolution: 3.283→39.647 Å / Num. obs: 94587 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Net I/σ(I): 15.7 |
| Reflection shell | Resolution: 3.283→3.4 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7664 / % possible all: 95.9 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.283→39.647 Å / SU ML: 0.45 / Phase error: 26.26 / 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: 3.283→39.647 Å
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| Refine LS restraints |
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| LS refinement shell |
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About Yorodumi



Human immunodeficiency virus type 1 group M subtype B
Homo sapiens (human)
X-RAY DIFFRACTION
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