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- EMDB-58588: Focused map of substrate engaged p97 in complex with Ufd1/Npl4 an... -

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Basic information

Entry
Database: EMDB / ID: EMD-58588
TitleFocused map of substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FAF1-State I (Npl4)
Map data
Sample
  • Complex: Substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FAF1- State I
KeywordsComplex / ATPase / Protein unfolding / Cell cycle / TRANSLOCASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsDrakonaki A / van den Boom J / Kroening A / Meyer H / Gatsogiannis C
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)424228829 Germany
German Research Foundation (DFG)509479817 Germany
German Research Foundation (DFG)496113311 Germany
German Research Foundation (DFG)DFG INST 211/667-1 Germany
German Research Foundation (DFG)INST-208767513-1_FUGG Germany
CitationJournal: Nat Commun / Year: 2026
Title: Structural dynamics of substrate processing by the p97-Ufd1-Npl4-FAF1 machinery.
Authors: Athina Drakonaki / Johannes van den Boom / Alexander Kröning / Hemmo Meyer / Christos Gatsogiannis /
Abstract: The AAA-ATPase VCP/p97 unfolds ubiquitylated proteins in key signaling and cellular homeostasis pathways, yet the mechanisms by which Ufd1-Npl4 and FAF1 adapters handle ubiquitin chains to coordinate ...The AAA-ATPase VCP/p97 unfolds ubiquitylated proteins in key signaling and cellular homeostasis pathways, yet the mechanisms by which Ufd1-Npl4 and FAF1 adapters handle ubiquitin chains to coordinate substrate loading and processing remain unclear. Our cryo-EM study of p97-Ufd1-Npl4 and FAF1 engaging a substrate reveal interactions that drive substrate processing. While Npl4 is capped by distal ubiquitins, and the initiator ubiquitin can be traced from the Npl4 groove to the ATPase channel at near-atomic resolution, we find that the Npl4 tower adaptively responds to the configurational changes in the ATPase motor's spiral staircase. A helix in FAF1 together with the Ufd1-UT3 domain engage proximal ubiquitins while providing the necessary structural plasticity to accommodate this motion and deliver ubiquitins to Npl4's groove. Our study reveals the intricate, dynamic interplay between p97, Ufd1-Npl4, and FAF1 in efficient processing of ubiquitylated substrates.
History
DepositionJun 16, 2026-
Header (metadata) releaseNov 4, 2026-
Map releaseNov 4, 2026-
UpdateNov 4, 2026-
Current statusNov 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58588.png

Downloads & links

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Map

FileDownload / File: emd_58588.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 576 pix.
= 453.888 Å		0.79 Å/pix.
x 576 pix.
= 453.888 Å		0.79 Å/pix.
x 576 pix.
= 453.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0218
Minimum - Maximum-0.08109046 - 0.155822
Average (Standard dev.)0.00012947792 (±0.004266172)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 453.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_58588_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_58588_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FA...

EntireName: Substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FAF1- State I
Components
  • Complex: Substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FAF1- State I

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Supramolecule #1: Substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FA...

SupramoleculeName: Substrate engaged p97 in complex with Ufd1/Npl4 and C-terminal FAF1- State I
type: complex / ID: 1 / Parent: 0
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

Concentration12 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
100.0 mMPotassium chlorideKCl
5.0 mMMagnesium chlorideMgCl2
0.5 mMTCEP
1.0 mMADP
1.0 mMBeryllium sulfateBeSO4
4.0 mMSodium fluorideNaF

Details: pH 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286.15 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 279701 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 270000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10568986
CTF correctionSoftware - Name: cryoSPARC (ver. v3.3-v4.6.2) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3-v4.6.2) / Number images used: 43423
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3-v4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3-v4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v3.3-v4.6.2)
FSC plot (resolution estimation)

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