+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27715 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / structural constituent of chromatin / nucleosome / nucleosome assembly / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / transcription cis-regulatory region binding / protein heterodimerization activity / DNA damage response / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.55 Å | |||||||||
Authors | Niklas HA / Rahman S / Worden EJ / Wolberger C | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome. Authors: Sanim Rahman / Niklas A Hoffmann / Evan J Worden / Marissa L Smith / Kevin E W Namitz / Bruce A Knutson / Michael S Cosgrove / Cynthia Wolberger / Abstract: The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core ...The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase, DR5, bBp5, sh2L, and PY-30, have revealed variability in the docking of MLL1-WRAD on nucleosomes. In addition, portions of the Ash2L structure and the position of DPY30 remain ambiguous. We used an integrated approach combining cryoelectron microscopy (cryo-EM) and mass spectrometry cross-linking to determine a structure of the MLL1-WRAD complex bound to ubiquitinated nucleosomes. The resulting model contains the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We also resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The docking of subunits in all four states differs from structures of MLL1-WRAD bound to unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_27715.map.gz | 9.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-27715-v30.xml emd-27715.xml | 28.2 KB 28.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27715_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_27715.png | 66.4 KB | ||
Masks | emd_27715_msk_1.map | 103 MB | Mask map | |
Others | emd_27715_additional_1.map.gz emd_27715_half_map_1.map.gz emd_27715_half_map_2.map.gz | 80.8 MB 80.8 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27715 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27715 | HTTPS FTP |
-Validation report
Summary document | emd_27715_validation.pdf.gz | 699.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_27715_full_validation.pdf.gz | 698.9 KB | Display | |
Data in XML | emd_27715_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_27715_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27715 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27715 | HTTPS FTP |
-Related structure data
Related structure data | 8du4MC 7ud5C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_27715.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_27715_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unsharpened map
File | emd_27715_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_27715_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_27715_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : RbBP5-WDR5 complex bound to the ubiquitinated nucleosome
+Supramolecule #1: RbBP5-WDR5 complex bound to the ubiquitinated nucleosome
+Supramolecule #2: RbBP5-WDR5 complex
+Supramolecule #3: Ubiquitinated nucleosome
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: WD repeat-containing protein 5
+Macromolecule #8: Retinoblastoma-binding protein 5
+Macromolecule #9: Polyubiquitin-B
+Macromolecule #5: 601 DNA (146-MER)
+Macromolecule #6: 601 DNA (146-MER)
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 5091 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |