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Yorodumi- PDB-1zla: X-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zla | ||||||
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Title | X-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bound to the nucleosomal core | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / Latency Associated Nuclear Antigen (LANA) / Kaposi's sarcoma Herpes Virus (KSHV) / Nucleosome core particle / chromatin / protein/protein interaction / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / host cell nucleus / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) Expression vector pET3-H2A (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Chodaparambil, J.V. / Barbera, A.J. / Kaye, K.M. / Luger, K. | ||||||
Citation | Journal: Science / Year: 2006 Title: The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA. Authors: Barbera, A.J. / Chodaparambil, J.V. / Kelley-Clarke, B. / Joukov, V. / Walter, J.C. / Luger, K. / Kaye, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zla.cif.gz | 325.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zla.ent.gz | 246.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zla_validation.pdf.gz | 516.4 KB | Display | wwPDB validaton report |
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Full document | 1zla_full_validation.pdf.gz | 559.8 KB | Display | |
Data in XML | 1zla_validation.xml.gz | 40.5 KB | Display | |
Data in CIF | 1zla_validation.cif.gz | 57.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/1zla ftp://data.pdbj.org/pub/pdb/validation_reports/zl/1zla | HTTPS FTP |
-Related structure data
Related structure data | 1aoiS 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
-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 15340.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 plysS / References: GenBank: 288992, UniProt: P84233*PLUS #3: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H4 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 plysS / References: UniProt: P62799 #4: Protein | Mass: 14181.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Expression vector pET3-H2A (others) / Gene: Histone H2A / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 plysS / References: GenBank: 30268540, UniProt: P06897*PLUS #5: Protein | Mass: 13794.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone H2B / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 plysS / References: GenBank: 296216, UniProt: P02281*PLUS |
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-DNA chain / Protein/peptide / Non-polymers , 3 types, 69 molecules IJK
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Alpha-Satellite DNA / Plasmid: pUC / Production host: Escherichia coli (E. coli) / Strain (production host): HB 101 #6: Protein/peptide | | Mass: 2260.646 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: N-terminal 1-23 amino acid region of Latency associated Nuclear Antigen (LANA)protein of Kaposi's Sarcoma Herpesvirus (KSHV) References: GenBank: 5669894, UniProt: Q9DUM3*PLUS #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.46 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Manganese chloride, Potassium chloride, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2005 / Details: mirrors |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 48638 / Num. obs: 47855 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 15273.7 / Redundancy: 2.66 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.99 |
Reflection shell | Resolution: 2.9→2.97 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.64 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1aoi Resolution: 2.9→50 Å / Cross valid method: Thorughout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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Xplor file |
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