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Open data
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Basic information
Entry | Database: PDB / ID: 4cy5 | ||||||
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Title | Crystal structure of the NSL1-WDS-NSL2 complex. | ||||||
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![]() | TRANSCRIPTION / EPIGENETIC REGULATOR / HISTONE ACETYLATION / CHROMATIN | ||||||
Function / homology | ![]() polytene chromosome interband / Formation of WDR5-containing histone-modifying complexes / haltere development / germarium-derived female germ-line cyst formation / Neddylation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / germ-line stem cell population maintenance / eye development / MLL3/4 complex ...polytene chromosome interband / Formation of WDR5-containing histone-modifying complexes / haltere development / germarium-derived female germ-line cyst formation / Neddylation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / germ-line stem cell population maintenance / eye development / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / neuromuscular junction development / histone acetyltransferase binding / oogenesis / regulation of endocytosis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / heart development / histone binding / chromatin remodeling / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dias, J. / Brettschneider, J. / Cusack, S. / Kadlec, J. | ||||||
![]() | ![]() Title: Structural Analysis of the Kansl1/Wdr5/Kansl2 Complex Reveals that Wdr5 is Required for Efficient Assembly and Chromatin Targeting of the Nsl Complex. Authors: Dias, J. / Van Nguyen, N. / Georgiev, P. / Gaub, A. / Brettschneider, J. / Cusack, S. / Kadlec, J. / Akhtar, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 55.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.5 KB | Display | ![]() |
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Full document | ![]() | 434.2 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cy1C ![]() 4cy2C ![]() 4cy3C ![]() 2g99S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 34673.297 Da / Num. of mol.: 1 / Fragment: RESIDUES 50-361 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1561.607 Da / Num. of mol.: 1 / Fragment: RESIDUES 155-166 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: Protein/peptide | Mass: 1768.003 Da / Num. of mol.: 1 / Fragment: RESIDUES 714-729 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() References: UniProt: A4V2Z1, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 0.44 % / Description: NONE |
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Crystal grow | pH: 6.6 Details: 20% (W/V) PEG 3350, 0.2 M DI-AMMONIUM TARTRATE, PH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97876 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 15438 / % possible obs: 99.4 % / Observed criterion σ(I): 2.3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.3 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2G99 Resolution: 2.3→37.11 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.314 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.275 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→37.11 Å
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Refine LS restraints |
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