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- EMDB-17466: Cryo-EM map of HECT E3 ligase UBR5 forming K48 linked ubiquitin chains -

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Basic information

Entry
Database: EMDB / ID: EMD-17466
TitleCryo-EM map of HECT E3 ligase UBR5 forming K48 linked ubiquitin chains
Map dataDeepEMhancer map of UBR5~UbD~UbA
Sample
  • Complex: HECT E3 UBR5 forming K48 linked Ubiquitin chains
    • Complex: Ubiquitin
      • Complex: Ubiquitin
KeywordsE3 ligase / UBR5 / Ubiquitination / UBQ / Ubiquitin / HECT / K48 / UBQ-chain / polyubiquitylation / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsHehl LA / Prabu JR / Schulman BA
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Chem Biol / Year: 2024
Title: Structural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5.
Authors: Laura A Hehl / Daniel Horn-Ghetko / J Rajan Prabu / Ronnald Vollrath / D Tung Vu / David A Pérez Berrocal / Monique P C Mulder / Gerbrand J van der Heden van Noort / Brenda A Schulman /
Abstract: Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron ...Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron microscopy (cryo-EM) to visualize stable mimics of the intermediates along K48-linked Ub chain formation by the human E3, UBR5. The structural data reveal a ≈ 620 kDa UBR5 dimer as the functional unit, comprising a scaffold with flexibly tethered Ub-associated (UBA) domains, and elaborately arranged HECT domains. Chains are forged by a UBA domain capturing an acceptor Ub, with its K48 lured into the active site by numerous interactions between the acceptor Ub, manifold UBR5 elements and the donor Ub. The cryo-EM reconstructions allow defining conserved HECT domain conformations catalyzing Ub transfer from E2 to E3 and from E3. Our data show how a full-length E3, ubiquitins to be adjoined, E2 and intermediary products guide a feed-forward HECT domain conformational cycle establishing a highly efficient, broadly targeting, K48-linked Ub chain forging machine.
History
DepositionMay 26, 2023-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17466.png

Downloads & links

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Map

FileDownload / File: emd_17466.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer map of UBR5~UbD~UbA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.77 Å/pix.
x 128 pix.
= 482.56 Å		3.77 Å/pix.
x 128 pix.
= 482.56 Å		3.77 Å/pix.
x 128 pix.
= 482.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0159
Minimum - Maximum-0.0011099855 - 1.3395554
Average (Standard dev.)0.0011754155 (±0.02048837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 482.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of UBR5~UbD~UbA

Fileemd_17466_half_map_1.map
AnnotationHalf map of UBR5~UbD~UbA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of UBR5~UbD~UbA

Fileemd_17466_half_map_2.map
AnnotationHalf map of UBR5~UbD~UbA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HECT E3 UBR5 forming K48 linked Ubiquitin chains

EntireName: HECT E3 UBR5 forming K48 linked Ubiquitin chains
Components
  • Complex: HECT E3 UBR5 forming K48 linked Ubiquitin chains
    • Complex: Ubiquitin
      • Complex: Ubiquitin

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Supramolecule #1: HECT E3 UBR5 forming K48 linked Ubiquitin chains

SupramoleculeName: HECT E3 UBR5 forming K48 linked Ubiquitin chains / type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 620 KDa

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Supramolecule #2: Ubiquitin

SupramoleculeName: Ubiquitin / type: complex / ID: 2 / Parent: 1 / Details: Donor Ubiquitin UbD
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9 KDa

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Supramolecule #3: Ubiquitin

SupramoleculeName: Ubiquitin / type: complex / ID: 3 / Parent: 2 / Details: Acceptor Ubiquitin UbA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9 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

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.3 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42761
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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