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- PDB-2ny5: HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T257S, V275... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ny5 | |||||||||
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Title | HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M) Complexed with CD4 and Antibody 17b | |||||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / HIV / gp120 / antibody / CD4 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX | |||||||||
Function / homology | ![]() 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 / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Dectin-2 family / 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 / coreceptor activity / positive regulation of calcium-mediated signaling / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of establishment of T cell polarity / T cell activation / positive regulation of interleukin-2 production / viral process / protein tyrosine kinase binding / host cell endosome membrane / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / MHC class II protein complex binding / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / early endosome / viral protein processing / cell adhesion / positive regulation of protein phosphorylation / immune response / membrane raft / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / external side of plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / virion attachment to host cell / endoplasmic reticulum membrane / protein kinase binding / host cell plasma membrane / structural molecule activity / virion membrane / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / protein homodimerization activity / extracellular space / zinc ion binding / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 388.1 KB | Display | ![]() |
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PDB format | ![]() | 315 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 826.5 KB | Display | ![]() |
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Full document | ![]() | 841 KB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 54.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nxyC ![]() 2nxzC ![]() 2ny0C ![]() 2ny1C ![]() 2ny2C ![]() 2ny3C ![]() 2ny4C ![]() 2ny6C ![]() 2ny7C ![]() 1gc1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules GC
#1: Protein | Mass: 35126.867 Da / Num. of mol.: 1 / Fragment: CORE Mutation: M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
-Antibody , 2 types, 2 molecules LH
#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.) ![]() Cell line (production host): Epstein-Barr virus immortalized B-cell clone fused with a murine B-cell fusion partner Production host: ![]() |
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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.) ![]() Cell line (production host): Epstein-Barr virus immortalized B-cell clone fused with a murine B-cell fusion partner Production host: ![]() |
-Sugars , 2 types, 10 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
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#6: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 320 molecules ![](data/chem/img/HOH.gif)
#7: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 9.2% PEG 4000, 9.5% MPD, 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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 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: 2.5→50 Å / Num. all: 44210 / Num. obs: 37534 / % possible obs: 84.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1GC1 Resolution: 2.5→48.97 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.895 / SU B: 19.497 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.689 / ESU R Free: 0.323 / 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: 39.921 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 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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