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- EMDB-17803: Consensus map - K48-linked ubiquitin chain formation with a culli... -

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Entry
Database: EMDB / ID: EMD-17803
TitleConsensus map - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide
Map dataDeepEMhancer sharpened map
Sample
  • Complex: Consensus map - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide
KeywordsCUL2 / FEM1C / ELOBC / SIL1 / Ubiquitin / Ubiquitin Ligase / Ubiquitin chain formation / Poliubiquitylation / E3 LIGASE / K48-linked chain formation / CDC34 / UBE2R2 / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsLiwocha J / Prabu JR / Kleiger G / Schulman BA
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases.
Authors: Joanna Liwocha / Jerry Li / Nicholas Purser / Chutima Rattanasopa / Samuel Maiwald / David T Krist / Daniel C Scott / Barbara Steigenberger / J Rajan Prabu / Brenda A Schulman / Gary Kleiger /
Abstract: E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked ...E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked poly-ubiquitin chains to control an enormous swath of eukaryotic biology. Yet the molecular mechanisms underlying this exceptional linkage specificity and millisecond kinetics of poly-ubiquitylation remain unclear. Here we obtain cryogenic-electron microscopy (cryo-EM) structures that provide pertinent insight into how such poly-ubiquitin chains are forged. The CRL RING domain not only activates the E2-bound ubiquitin but also shapes the conformation of a distinctive UBE2R2 loop, positioning both the ubiquitin to be transferred and the substrate-linked acceptor ubiquitin within the active site. The structures also reveal how the ubiquitin-like protein NEDD8 uniquely activates CRLs during chain formation. NEDD8 releases the RING domain from the CRL, but unlike previous CRL-E2 structures, does not contact UBE2R2. These findings suggest how poly-ubiquitylation may be accomplished by many E2s and E3s.
History
DepositionJul 7, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17803.png

Downloads & links

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Map

FileDownload / File: emd_17803.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 380 pix.
= 323.38 Å		0.85 Å/pix.
x 380 pix.
= 323.38 Å		0.85 Å/pix.
x 380 pix.
= 323.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.851 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0593
Minimum - Maximum-0.045708492 - 1.9840711
Average (Standard dev.)0.0011149897 (±0.023459028)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 323.38 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17803_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Relion PostProcessed Map

Fileemd_17803_additional_1.map
AnnotationRelion PostProcessed Map
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Half map: #2

Fileemd_17803_half_map_1.map
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Half map: #1

Fileemd_17803_half_map_2.map
Projections & Slices
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Sample components

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Entire : Consensus map - K48-linked ubiquitin chain formation with a culli...

EntireName: Consensus map - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide
Components
  • Complex: Consensus map - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

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Supramolecule #1: Consensus map - K48-linked ubiquitin chain formation with a culli...

SupramoleculeName: Consensus map - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 190 KDa

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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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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: 2.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5n4w

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61956
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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