+Open data
-Basic information
Entry | Database: PDB / ID: 1jek | ||||||
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Title | Visna TM CORE STRUCTURE | ||||||
Components | (ENV POLYPROTEINEnv (gene)) x 2 | ||||||
Keywords | VIRAL PROTEIN / ENVELOPE GLYCOPROTEIN / RETROVIRUS / HIV / SIV / GP41 | ||||||
Function / homology | Function and homology information membrane => GO:0016020 / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Malashkevich, V.N. / Singh, M. / Kim, P.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: The trimer-of-hairpins motif in membrane fusion: Visna virus. Authors: Malashkevich, V.N. / Singh, M. / Kim, P.S. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Crystal Structure of the Simian Immunodeficiency Virus (Siv) Gp41 Core: Conserved Helical Interactions Underlie the Broad Inhibitory Activity of Gp41 Peptides Authors: Malashkevich, V.N. / Chan, D.C. / Chutkowski, C.T. / Kim, P.S. #2: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Core Structure of Gp41 from the HIV Envelope Glycoprotein Authors: Chan, D.C. / Fass, D. / Berger, J.M. / Kim, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jek.cif.gz | 30.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jek.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/1jek ftp://data.pdbj.org/pub/pdb/validation_reports/je/1jek | HTTPS FTP |
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-Related structure data
Related structure data | 2sivS 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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Unit cell |
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Components on special symmetry positions |
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Details | Trimer is formed around the crystallographic 3-fold axis |
-Components
#1: Protein/peptide | Mass: 4336.971 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Visna virus. References: UniProt: P35954 |
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#2: Protein/peptide | Mass: 4126.549 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Visna virus. References: UniProt: P35954 |
#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: 2.91 Å3/Da / Density % sol: 57.67 % / Description: POLYSERINE MODEL | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% tert-butanol, 0.1M TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.28 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25 Å / Num. obs: 16300 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.5→1.52 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.138 / % possible all: 64.7 |
Reflection | *PLUS Num. measured all: 52353 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / % possible obs: 64.7 % / Rmerge(I) obs: 0.259 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2SIV Resolution: 1.5→9.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 914104.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 94.78 Å2 / ksol: 0.451 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→9.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.363 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.319 / Rfactor obs: 0.319 |