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Yorodumi- PDB-3cyo: Structure of a longer thermalstable core domain of HIV-1 GP41 con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cyo | ||||||
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Title | Structure of a longer thermalstable core domain of HIV-1 GP41 containing the enfuvirtide resistance mutation N43D and complementary mutation E137K | ||||||
Components | Transmembrane protein | ||||||
Keywords | VIRAL PROTEIN / HIV-1 ENVELOPE GLYCOPROTEIN / 6-HELIX BUNDLE / GP41 / N43D / E137K / AIDS / APOPTOSIS / COILED COIL / ENVELOPE PROTEIN / FUSION PROTEIN / HOST-VIRUS INTERACTION / MEMBRANE / TRANSMEMBRANE / VIRION / Cleavage on pair of basic residues / Lipoprotein / Palmitate / Viral immunoevasion | ||||||
Function / homology | Function and homology information Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wang, Z.M. / Dwyer, J.J. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Impact of the enfuvirtide resistance mutation N43D and the associated baseline polymorphism E137K on peptide sensitivity and six-helix bundle structure. Authors: Bai, X. / Wilson, K.L. / Seedorff, J.E. / Ahrens, D. / Green, J. / Davison, D.K. / Jin, L. / Stanfield-Oakley, S.A. / Mosier, S.M. / Melby, T.E. / Cammack, N. / Wang, Z. / Greenberg, M.L. / Dwyer, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cyo.cif.gz | 27 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cyo.ent.gz | 17.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/3cyo ftp://data.pdbj.org/pub/pdb/validation_reports/cy/3cyo | HTTPS FTP |
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-Related structure data
Related structure data | 2ot5C 3cp1C 1envS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9975.190 Da / Num. of mol.: 1 Fragment: FUSION PROTEIN OF UNP RESIDUES 536-579, LINKER, AND UNP RESIDUES 628-663 Mutation: N554D,E648K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: env / Plasmid: PET41A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q70626, UniProt: Q53I19*PLUS |
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#2: 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: 1.74 Å3/Da / Density % sol: 29.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25-40% ETHYLENE GLYCOL, 0.2 M MGCL2 AND 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 1, 2007 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 4263 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Rsym value: 0.096 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.879 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ENV Resolution: 2.1→50 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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