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Yorodumi- PDB-7w67: The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w67 | ||||||||||||||||||
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Title | The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide | ||||||||||||||||||
Components |
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Keywords | PROTEIN BINDING / MLL family methyltransferases / product specificity / F/Y switch | ||||||||||||||||||
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 / regulation of short-term neuronal synaptic plasticity / MLL3/4 complex / Set1C/COMPASS complex ...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 / regulation of short-term neuronal synaptic plasticity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / T-helper 2 cell differentiation / definitive hemopoiesis / histone H3K4 methyltransferase activity / : / embryonic hemopoiesis / anterior/posterior pattern specification / exploration behavior / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / hemopoiesis / MLL1 complex / nucleosomal DNA binding / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / transcription initiation-coupled chromatin remodeling / spleen development / cellular response to transforming growth factor beta stimulus / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / circadian regulation of gene expression / euchromatin / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / protein modification process / visual learning / PKMTs methylate histone lysines / beta-catenin binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / histone binding / fibroblast proliferation / positive regulation of cell growth / protein-containing complex assembly / transcription cis-regulatory region binding / protein heterodimerization activity / apoptotic process / DNA damage response / chromatin binding / positive regulation of cell population proliferation / nucleolus / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å | ||||||||||||||||||
Authors | Zhao, L. / Li, Y. / Chen, Y. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Mol.Cell / Year: 2022 Title: Structural basis for product specificities of MLL family methyltransferases. Authors: Li, Y. / Zhao, L. / Zhang, Y. / Wu, P. / Xu, Y. / Mencius, J. / Zheng, Y. / Wang, X. / Xu, W. / Huang, N. / Ye, X. / Lei, M. / Shi, P. / Tian, C. / Peng, C. / Li, G. / Liu, Z. / Quan, S. / Chen, Y. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w67.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w67.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 7w67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/7w67 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/7w67 | HTTPS FTP |
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-Related structure data
Related structure data | 7w6aC 7w6iC 7w6jC 7w6lC 5f6lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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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-Components
-Protein , 2 types, 2 molecules AC
#1: Protein | Mass: 20597.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASH2L, ASH2L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBL3 |
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#2: Protein | Mass: 18227.129 Da / Num. of mol.: 1 / Mutation: N3861I,Q3867L,C3882SS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1 / Production host: Escherichia coli (E. coli) References: UniProt: Q03164, [histone H3]-lysine4 N-methyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases |
-Protein/peptide , 2 types, 2 molecules FM
#3: Protein/peptide | Mass: 3255.321 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP5, RBQ3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15291 |
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#4: Protein/peptide | Mass: 1063.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2 |
-Non-polymers , 3 types, 130 molecules
#5: Chemical | ChemComp-SAH / |
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#6: Chemical | ChemComp-ZN / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.05 Å3/Da / Density % sol: 45.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 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: 0.9785 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.194→50 Å / Num. obs: 19701 / % possible obs: 99.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.048 / Rrim(I) all: 0.121 / Χ2: 0.962 / Net I/σ(I): 5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F6L Resolution: 2.194→31.889 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.85 / 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: 97.5 Å2 / Biso mean: 48.0675 Å2 / Biso min: 25.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.194→31.889 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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