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- 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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![]() | IMMUNE SYSTEM / Protein-Protein complex / IgG / Anti-HIV antibodies / gp120 | ||||||||||||
Function / homology | ![]() IgD immunoglobulin complex / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / maintenance of protein location in cell / T cell selection / MHC class II protein binding ...IgD immunoglobulin complex / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / maintenance of protein location in cell / T cell selection / MHC class II protein binding / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / CD22 mediated BCR regulation / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / regulation of T cell activation / Other interleukin signaling / extracellular matrix structural constituent / Classical antibody-mediated complement activation / T cell receptor complex / immunoglobulin complex / Initial triggering of complement / enzyme-linked receptor protein signaling pathway / Dectin-2 family / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / immunoglobulin mediated immune response / macrophage differentiation / regulation of calcium ion transport / Generation of second messenger molecules / T cell differentiation / FCGR activation / Co-inhibition by PD-1 / positive regulation of protein kinase activity / Role of LAT2/NTAL/LAB on calcium mobilization / Binding and entry of HIV virion / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / coreceptor activity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / FCERI mediated Ca+2 mobilization / positive regulation of interleukin-2 production / FCGR3A-mediated IL10 synthesis / positive regulation of calcium-mediated signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / host cell endosome membrane / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / Regulation of actin dynamics for phagocytic cup formation / positive regulation of T cell activation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class II protein complex binding / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / positive regulation of protein phosphorylation / virus receptor activity / positive regulation of cell growth / defense response to Gram-negative bacterium / blood microparticle / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / early endosome / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / 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 / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / virion attachment to host cell Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Garces, F. / Wilson, I.A. | ||||||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 724.6 KB | Display | ![]() |
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PDB format | ![]() | 601.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 156.4 KB | Display | |
Data in CIF | ![]() | 199.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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.) ![]() Strain: isolate JRCSF / Gene: env / Cell line (production host): 293 FreeStyle / Production host: ![]() #2: Protein | Mass: 20419.252 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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.) ![]() ![]() #4: Antibody | Mass: 25460.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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: ![]()
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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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