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- EMDB-46742: Structure of UBR4-KCMF1-CaM E3 ligase complex (+ UBE2A) -

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Basic information

Entry
Database: EMDB / ID: EMD-46742
TitleStructure of UBR4-KCMF1-CaM E3 ligase complex (+ UBE2A)
Map data
Sample
  • Complex: Structure of UBR4-KCMF1-CaM E3 ligase complex (+ UBE2A)
    • Complex: E2 ligase UBE2A
KeywordsE3 ligase / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYang Z / Haakonsen DL / Rape M
Funding support United States, 2 items
OrganizationGrant numberCountry
The G. Harold and Leila Y. Mathers Foundation United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2025
Title: Molecular basis of SIFI activity in the integrated stress response.
Authors: Zhi Yang / Diane L Haakonsen / Michael Heider / Samuel R Witus / Alex Zelter / Tobias Beschauner / Michael J MacCoss / Michael Rapé /
Abstract: Chronic stress response activation impairs cell survival and causes devastating degenerative diseases. Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase silencing factor ...Chronic stress response activation impairs cell survival and causes devastating degenerative diseases. Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase silencing factor of the integrated stress response (SIFI), to terminate stress response signalling and ensure cellular homeostasis. How a silencing factor can sense stress across cellular scales to elicit timely stress response inactivation is poorly understood. Here we combine cryo-electron microscopy analysis of endogenous SIFI with AlphaFold modelling and biochemical studies to report the structural and mechanistic basis of the silencing of the integrated stress response. SIFI detects both stress indicators and stress response components through flexible domains within an easily accessible scaffold, before building linkage-specific ubiquitin chains at separate, sterically restricted elongation modules. Ubiquitin handover by a ubiquitin-like domain couples versatile substrate modification to linkage-specific ubiquitin polymer formation. Stress response silencing therefore exploits a catalytic mechanism that is geared towards processing many diverse proteins and therefore allows a single enzyme to monitor and, if needed, modulate a complex cellular state.
History
DepositionAug 25, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46742.png

Downloads & links

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Map

FileDownload / File: emd_46742.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 560 pix.
= 474.88 Å		0.85 Å/pix.
x 560 pix.
= 474.88 Å		0.85 Å/pix.
x 560 pix.
= 474.88 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.68712527 - 1.234015
Average (Standard dev.)0.00030070244 (±0.018985681)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 474.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46742_msk_1.map
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Additional map: low-pass filtered map

Fileemd_46742_additional_1.map
Annotationlow-pass filtered map
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Half map: #2

Fileemd_46742_half_map_1.map
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Half map: #1

Fileemd_46742_half_map_2.map
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Sample components

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Entire : Structure of UBR4-KCMF1-CaM E3 ligase complex (+ UBE2A)

EntireName: Structure of UBR4-KCMF1-CaM E3 ligase complex (+ UBE2A)
Components
  • Complex: Structure of UBR4-KCMF1-CaM E3 ligase complex (+ UBE2A)
    • Complex: E2 ligase UBE2A

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Supramolecule #1: Structure of UBR4-KCMF1-CaM E3 ligase complex (+ UBE2A)

SupramoleculeName: Structure of UBR4-KCMF1-CaM E3 ligase complex (+ UBE2A)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.4 kDa/nm

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Supramolecule #2: E2 ligase UBE2A

SupramoleculeName: E2 ligase UBE2A / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.3) / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 82034
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
FSC plot (resolution estimation)

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