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Yorodumi- PDB-6psa: PIE12 D-PEPTIDE AGAINST HIV ENTRY (IN COMPLEX WITH IQN17 Q577R RE... -
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-Basic information
Entry | Database: PDB / ID: 6psa | ||||||
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Title | PIE12 D-PEPTIDE AGAINST HIV ENTRY (IN COMPLEX WITH IQN17 Q577R RESISTANCE MUTANT) | ||||||
Components |
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Keywords | VIRAL PROTEIN/INHIBITOR / HIV / HELIX / HIV ENTRY INHIBITOR / IQN17 PIE12 / D-PEPTIDE INHIBITOR / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information Synthesis and processing of ENV and VPU / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / evasion of host immune response / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter ...Synthesis and processing of ENV and VPU / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / evasion of host immune response / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Alpha-defensins / Oxidative Stress Induced Senescence / Dectin-2 family / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / Binding and entry of HIV virion / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / cellular response to amino acid starvation / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / clathrin-dependent endocytosis of virus by host cell / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / viral protein processing / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / symbiont entry into host cell / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / chromatin binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / nucleus Similarity search - Function | ||||||
Biological species | synthetic construct (others) Saccharomyces cerevisiae (brewer's yeast) Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Hill, C.P. / Whitby, F.G. / Kay, M. / Weinstock, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Retrovirology / Year: 2019 Title: Characterization of resistance to a potent D-peptide HIV entry inhibitor. Authors: Smith, A.R. / Weinstock, M.T. / Siglin, A.E. / Whitby, F.G. / Francis, J.N. / Hill, C.P. / Eckert, D.M. / Root, M.J. / Kay, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6psa.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6psa.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 6psa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6psa_validation.pdf.gz | 427.1 KB | Display | wwPDB validaton report |
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Full document | 6psa_full_validation.pdf.gz | 427.3 KB | Display | |
Data in XML | 6psa_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 6psa_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/6psa ftp://data.pdbj.org/pub/pdb/validation_reports/ps/6psa | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Polypeptide(D) | Mass: 2029.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
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#2: Protein/peptide | Mass: 5542.534 Da / Num. of mol.: 1 Fragment: GP41 HYDROPHOBIC POCKET, RESIDUES 565-581, GCN4, RESIDUES 249-276 Mutation: Q577R / Source method: obtained synthetically Source: (synth.) Saccharomyces cerevisiae (brewer's yeast), (synth.) Human immunodeficiency virus type 1 References: UniProt: P03069, UniProt: P04578 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.01 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: HAMPTON RESEARCH SALT RX SCREEN, CONDITION B4 - 1.8M AMMONIUM CITRATE DIBASIC, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6 Temp details: K |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97591 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2011 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97591 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 14574 / % possible obs: 98.5 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.375 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→13.21 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.07
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Solvent computation | Shrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Bsol: 66.47 Å2 / ksol: 0.56 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→13.21 Å
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Refine LS restraints |
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LS refinement shell |
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