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Yorodumi- PDB-5f5e: The Crystal Structure of MLL1 SET domain with N3816I/Q3867L mutation -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f5e | ||||||
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Title | The Crystal Structure of MLL1 SET domain with N3816I/Q3867L mutation | ||||||
Components | Histone-lysine N-methyltransferase 2A | ||||||
Keywords | TRANSFERASE / histone methyltransferase / histone methylation / SET domain | ||||||
Function / homology | Function and homology information protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / T-helper 2 cell differentiation / regulation of short-term neuronal synaptic plasticity / definitive hemopoiesis ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / T-helper 2 cell differentiation / regulation of short-term neuronal synaptic plasticity / definitive hemopoiesis / histone H3K4 methyltransferase activity / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / spleen development / lysine-acetylated histone binding / cellular response to transforming growth factor beta stimulus / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / Transcriptional regulation of granulopoiesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / circadian regulation of gene expression / PKMTs methylate histone lysines / visual learning / protein modification process / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / protein-containing complex assembly / methylation / chromatin binding / positive regulation of DNA-templated transcription / apoptotic process / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.802 Å | ||||||
Model details | histone methylation, histone methyltransferase | ||||||
Authors | Li, Y. / Lei, M. / Chen, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2016 Title: Structural basis for activity regulation of MLL family methyltransferases. Authors: Li, Y. / Han, J. / Zhang, Y. / Cao, F. / Liu, Z. / Li, S. / Wu, J. / Hu, C. / Wang, Y. / Shuai, J. / Chen, J. / Cao, L. / Li, D. / Shi, P. / Tian, C. / Zhang, J. / Dou, Y. / Li, G. / Chen, Y. / Lei, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f5e.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f5e.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 5f5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f5e_validation.pdf.gz | 832.1 KB | Display | wwPDB validaton report |
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Full document | 5f5e_full_validation.pdf.gz | 833.9 KB | Display | |
Data in XML | 5f5e_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 5f5e_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/5f5e ftp://data.pdbj.org/pub/pdb/validation_reports/f5/5f5e | HTTPS FTP |
-Related structure data
Related structure data | 5f59C 5f6kC 5f6lC 2w5yS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18243.195 Da / Num. of mol.: 1 / Fragment: MLL1 SET domain (UNP RESIDUES 3813-3969) / Mutation: N3861I, Q3867L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1 / Plasmid: pET28b-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: Q03164, histone-lysine N-methyltransferase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SAH / |
#4: 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: 2.53 Å3/Da / Density % sol: 51.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 35% Tacsimate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 17325 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.031 / Rrim(I) all: 0.096 / Χ2: 1.331 / Net I/av σ(I): 36.519 / Net I/σ(I): 6.5 / Num. measured all: 166463 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W5Y Resolution: 1.802→28.068 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.81 Å2 / Biso mean: 45.1431 Å2 / Biso min: 19.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.802→28.068 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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