+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23738 | |||||||||
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Title | Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 | |||||||||
Map data | Mode01 | |||||||||
Sample |
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Keywords | MLL1-NCP / H3K4 methylation / TRANSFERASE / TRANSFERASE-DNA BINDING PROTEIN-DNA complex | |||||||||
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 / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity ...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 / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity / Set1C/COMPASS complex / MLL1/2 complex / definitive hemopoiesis / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / embryonic hemopoiesis / Cardiogenesis / anterior/posterior pattern specification / exploration behavior / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / hemopoiesis / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / positive regulation of gluconeogenesis / spleen development / cellular response to transforming growth factor beta stimulus / methylated histone binding / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / skeletal system development / gluconeogenesis / Deactivation of the beta-catenin transactivating complex / lysine-acetylated histone binding / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / euchromatin / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / 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 / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / HATs acetylate histones / histone binding / fibroblast proliferation / protein-containing complex assembly / methylation / regulation of cell cycle / transcription cis-regulatory region binding / protein heterodimerization activity / DNA damage response / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM | |||||||||
Authors | Park SH / Ayoub A | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Biochemistry / Year: 2022 Title: Regulation of MLL1 Methyltransferase Activity in Two Distinct Nucleosome Binding Modes. Authors: Alex Ayoub / Sang Ho Park / Young-Tae Lee / Uhn-Soo Cho / Yali Dou / Abstract: Cryo-EM structures of the KMT2A/MLL1 core complex bound on nucleosome core particles (NCPs) suggest unusual rotational dynamics of the MLL1 complex approaching its physiological substrate. However, ...Cryo-EM structures of the KMT2A/MLL1 core complex bound on nucleosome core particles (NCPs) suggest unusual rotational dynamics of the MLL1 complex approaching its physiological substrate. However, the functional implication of such dynamics remains unclear. Here, we show that the MLL1 core complex also shows high rotational dynamics bound on the NCP carrying the catalytically inert histone H3 lysine 4 to methionine (K4M) mutation. There are two major binding modes of the MLL1 complex on the NCP. Importantly, disruption of only one of the binding modes compromised the overall MLL1 activity in an NCP-specific manner. We propose that the MLL1 core complex probably exists in an equilibrium of poised and active binding modes. The high rotational dynamics of the MLL1 complex on the NCP is a feature that can be exploited for loci-specific regulation of H3K4 methylation in higher eukaryotes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23738.map.gz | 11.5 MB | EMDB map data format | |
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Header (meta data) | emd-23738-v30.xml emd-23738.xml | 23.1 KB 23.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23738_fsc.xml | 16.2 KB | Display | FSC data file |
Images | emd_23738.png | 55.8 KB | ||
Filedesc metadata | emd-23738.cif.gz | 7.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23738 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23738 | HTTPS FTP |
-Validation report
Summary document | emd_23738_validation.pdf.gz | 379.6 KB | Display | EMDB validaton report |
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Full document | emd_23738_full_validation.pdf.gz | 379.2 KB | Display | |
Data in XML | emd_23738_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | emd_23738_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23738 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23738 | HTTPS FTP |
-Related structure data
Related structure data | 7mbmMC 7mbnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23738.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mode01 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nu...
+Supramolecule #1: MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nu...
+Supramolecule #2: RbBP5, WDR5, SET1, and ASH2L
+Supramolecule #3: nucleosome
+Macromolecule #1: Retinoblastoma-binding protein 5
+Macromolecule #2: WD repeat-containing protein 5
+Macromolecule #3: Histone-lysine N-methyltransferase 2A
+Macromolecule #4: Set1/Ash2 histone methyltransferase complex subunit ASH2
+Macromolecule #5: Histone H3
+Macromolecule #6: Histone H4
+Macromolecule #7: Histone H2A
+Macromolecule #8: Histone H2B 1.1
+Macromolecule #9: DNA (145-MER)
+Macromolecule #10: DNA (145-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 53.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-7mbm: |