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- EMDB-27802: Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome- State 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-27802
TitleComplex between MLL1-WRAD and an H2B-ubiquitinated nucleosome- State 1
Map data
Sample
  • Complex: RBBP5 bound to an H2B-ubiquitinated nucleosome
    • Complex: nucleosome
    • Complex: MLL1 WRAD complex
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsNiklas HA / Rahman S / Worden EJ / Wolberger C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM130393 United States
CitationJournal: 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
DepositionAug 8, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27802.png

Downloads & links

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Map

FileDownload / File: emd_27802.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 317.4 Å		1.06 Å/pix.
x 300 pix.
= 317.4 Å		1.06 Å/pix.
x 300 pix.
= 317.4 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
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Contour LevelBy AUTHOR: 0.0138
Minimum - Maximum-0.08180453 - 0.14172164
Average (Standard dev.)0.00012922137 (±0.0027129748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27802_msk_1.map
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Additional map: Unsharpened map

Fileemd_27802_additional_1.map
AnnotationUnsharpened map
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Half map: #2

Fileemd_27802_half_map_1.map
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Half map: #1

Fileemd_27802_half_map_2.map
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Sample components

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Entire : RBBP5 bound to an H2B-ubiquitinated nucleosome

EntireName: RBBP5 bound to an H2B-ubiquitinated nucleosome
Components
  • Complex: RBBP5 bound to an H2B-ubiquitinated nucleosome
    • Complex: nucleosome
    • Complex: MLL1 WRAD complex

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Supramolecule #1: RBBP5 bound to an H2B-ubiquitinated nucleosome

SupramoleculeName: RBBP5 bound to an H2B-ubiquitinated nucleosome / type: complex / Chimera: Yes / ID: 1 / Parent: 0

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Supramolecule #2: nucleosome

SupramoleculeName: nucleosome / type: complex / Chimera: Yes / ID: 2 / Parent: 1
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: MLL1 WRAD complex

SupramoleculeName: MLL1 WRAD complex / type: complex / Chimera: Yes / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5091 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8140


Details: rescaled and low pass-filtered to 60A
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103849
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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