+Open data
-Basic information
Entry | Database: PDB / ID: 6jqk | ||||||
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Title | Structure of C34M/N36 | ||||||
Components |
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Keywords | VIRAL PROTEIN / HIV / envlope / T20 | ||||||
Function / homology | Function and homology information Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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 / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å | ||||||
Authors | Yu, D.W. / Qin, B. | ||||||
Citation | Journal: To Be Published Title: Structure of C34M/N36 Authors: Yu, D.W. / Qin, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jqk.cif.gz | 31.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jqk.ent.gz | 20.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jqk_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 6jqk_full_validation.pdf.gz | 431.1 KB | Display | |
Data in XML | 6jqk_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 6jqk_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/6jqk ftp://data.pdbj.org/pub/pdb/validation_reports/jq/6jqk | HTTPS FTP |
-Related structure data
Related structure data | 1aikS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 4152.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS |
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#2: Protein/peptide | Mass: 4221.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS |
#3: 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: 1.75 Å3/Da / Density % sol: 29.8 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M Sodium chloride,0.1 M BIS-TRIS pH 5.5,25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2018 |
Radiation | Monochromator: SI(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 1.498→38.48 Å / Num. obs: 9811 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.96 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Net I/σ(I): 20.34 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.43 / Num. unique obs: 1561 / CC1/2: 0.967 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AIK Resolution: 1.498→38.48 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.498→38.48 Å
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Refine LS restraints |
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LS refinement shell |
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