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Yorodumi- PDB-2nxy: HIV-1 gp120 Envelope Glycoprotein(S334A) Complexed with CD4 and A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nxy | ||||||
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Title | HIV-1 gp120 Envelope Glycoprotein(S334A) Complexed with CD4 and Antibody 17b | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HIV / gp120 / antibody / CD4 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | Function and homology information helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / extracellular matrix structural constituent / T cell receptor complex / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / immunoglobulin complex, circulating / coreceptor activity / immunoglobulin receptor binding / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / positive regulation of calcium-mediated signaling / viral process / positive regulation of interleukin-2 production / protein tyrosine kinase binding / complement activation, classical pathway / clathrin-coated endocytic vesicle membrane / antigen binding / Vpu mediated degradation of CD4 / calcium-mediated signaling / transmembrane signaling receptor activity / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / Clathrin-mediated endocytosis / virus receptor activity / Downstream TCR signaling / MHC class II protein complex binding / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / antibacterial humoral response / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / blood microparticle / cell surface receptor signaling pathway / positive regulation of viral entry into host cell / early endosome / cell adhesion / positive regulation of protein phosphorylation / membrane raft / immune response / endoplasmic reticulum lumen / external side of plasma membrane / lipid binding / viral envelope / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / protein kinase binding / enzyme binding / signal transduction / protein homodimerization activity / extracellular space / zinc ion binding / extracellular exosome / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhou, T. / Xu, L. / Dey, B. / Hessell, A.J. / Van Ryk, D. / Xiang, S.H. / Yang, X. / Zhang, M.Y. / Zwick, M.B. / Arthos, J. ...Zhou, T. / Xu, L. / Dey, B. / Hessell, A.J. / Van Ryk, D. / Xiang, S.H. / Yang, X. / Zhang, M.Y. / Zwick, M.B. / Arthos, J. / Burton, D.R. / Dimitrov, D.S. / Sodroski, J. / Wyatt, R. / Nabel, G.J. / Kwong, P.D. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Structural definition of a conserved neutralization epitope on HIV-1 gp120. Authors: Zhou, T. / Xu, L. / Dey, B. / Hessell, A.J. / Van Ryk, D. / Xiang, S.H. / Yang, X. / Zhang, M.Y. / Zwick, M.B. / Arthos, J. / Burton, D.R. / Dimitrov, D.S. / Sodroski, J. / Wyatt, R. / Nabel, G.J. / Kwong, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nxy.cif.gz | 396 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nxy.ent.gz | 320.7 KB | Display | PDB format |
PDBx/mmJSON format | 2nxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nxy_validation.pdf.gz | 501.4 KB | Display | wwPDB validaton report |
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Full document | 2nxy_full_validation.pdf.gz | 514.3 KB | Display | |
Data in XML | 2nxy_validation.xml.gz | 44.4 KB | Display | |
Data in CIF | 2nxy_validation.cif.gz | 65.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/2nxy ftp://data.pdbj.org/pub/pdb/validation_reports/nx/2nxy | HTTPS FTP |
-Related structure data
Related structure data | 2nxzC 2ny0C 2ny1C 2ny2C 2ny3C 2ny4C 2ny5C 2ny6C 2ny7C 1g9cS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 35040.688 Da / Num. of mol.: 1 / Fragment: CORE / Mutation: S334A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: HXBc2 / Plasmid: CMVR / Cell line (production host): embryonic cell line 293 / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: Q49DS8 |
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#2: Protein | Mass: 20419.252 Da / Num. of mol.: 1 / Fragment: D1D2, N-TERMINAL TWO DOMAIN FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: Escherichia coli (E. coli) / References: UniProt: P01730 |
-Antibody , 2 types, 2 molecules CD
#3: Antibody | Mass: 23399.898 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Cell line (production host): Epstein-Barr virus immortalized B-cell clone fused with a murine B-cell fusion partner Production host: Homo sapiens (human) / References: UniProt: Q6P5S8 |
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#4: Antibody | Mass: 24457.387 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Cell line (production host): Epstein-Barr virus immortalized B-cell clone fused with a murine B-cell fusion partner Production host: Homo sapiens (human) / References: UniProt: Q6N095 |
-Sugars , 1 types, 13 molecules
#5: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 810 molecules
#6: Chemical | #7: Chemical | ChemComp-TRS / | #8: 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: 2.98 Å3/Da / Density % sol: 58.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 7.0 % PEG 8000, 7.5 % 1,6-Hexanediol, 100 mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 225 mm / Detector: CCD / Date: Jun 4, 2003 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. all: 84467 / Num. obs: 82862 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1G9C Resolution: 2→35.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.641 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Authors state that because crystals were small and subject to high radiation dosages during data collection, difference fouriers comparing the initial and final swatches of data were ...Details: Authors state that because crystals were small and subject to high radiation dosages during data collection, difference fouriers comparing the initial and final swatches of data were inspected to identify radiation-induced disulfide breakage, and the refined models were adjusted to reflect the initial, radiation-damage free structure. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.147 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.049 Å / Total num. of bins used: 20
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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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