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- EMDB-54584: Arabidopsis thaliana TPLATE complex negative stain EM map -

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Basic information

Entry
Database: EMDB / ID: EMD-54584
TitleArabidopsis thaliana TPLATE complex negative stain EM map
Map dataThis map is a reconstruction from negative stain EM data
Sample
  • Complex: TPLATE complex
Keywordsendocytosis / plant / adaptor protein complex / TPLATE complex
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsKraus JM / Van Damme D / Pleskot R / Neubergerova M
Funding supportEuropean Union, Belgium, Czech Republic, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)682436European Union
Research Foundation - Flanders (FWO)G017919N Belgium
Czech Science Foundation22-35680M Czech Republic
CitationJournal: Nat Plants / Year: 2025
Title: A combined biochemical and computational approach provides evidence for membrane remodelling by the structural scaffold of the endocytic TPLATE complex.
Authors: Julia M Kraus / Michaela Neubergerová / Alvaro Furones Cuadrado / Neeltje Schilling / Dominique Eeckhout / Nancy De Winne / Eveline Van De Slijke / Michaël Vandorpe / Klaas Yperman / ...Authors: Julia M Kraus / Michaela Neubergerová / Alvaro Furones Cuadrado / Neeltje Schilling / Dominique Eeckhout / Nancy De Winne / Eveline Van De Slijke / Michaël Vandorpe / Klaas Yperman / Evelien Mylle / Marcus Fislage / Geert De Jaeger / Roman Pleskot / Daniël Van Damme /
Abstract: Eukaryotic cells maintain homeostasis of their outer membrane by controlled internalization of lipid and protein constituents via endocytosis. Endocytosis is evolutionary conserved and uses similarly ...Eukaryotic cells maintain homeostasis of their outer membrane by controlled internalization of lipid and protein constituents via endocytosis. Endocytosis is evolutionary conserved and uses similarly folded domains. How these structural folds are combined into proteins and protein complexes, however, differs between eukaryotic kingdoms. The TPLATE complex (TPC) in plants is an evolutionary ancient protein module that combines several protein domains with a conserved role in endocytosis into a single octameric protein complex. Its molecular architecture, lipid-nucleated condensate formation and requirement for clathrin cage curvature revealed its function in endocytosis initiation in plants. Mechanistic understanding of how this complex drives membrane deformation during plant endocytosis is, however, lacking. Here we used an integrative structural approach to obtain a precise molecular structure of the TPC of Arabidopsis thaliana. In addition, our approach allowed visualizing the structural flexibility that hallmarks this enigmatic complex. We prove that the intrinsic structural flexibility is required for its functionality and membrane recruitment. The membrane-binding interface consists of several domains with differential lipid preferences. Finally, we demonstrate via molecular dynamics simulations that the crescent shape of the structured part of the complex is sufficient for membrane curvature generation. Our mechanistic insight, obtained by a combined biochemical and computational approach, shows that the structured part of the TPC likely contributes to the execution of plant endocytosis, which does not depend on cytoskeletal-based force generation.
History
DepositionJul 28, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54584.png

Downloads & links

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Map

FileDownload / File: emd_54584.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map is a reconstruction from negative stain EM data
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.94 Å/pix.
x 180 pix.
= 349.2 Å		1.94 Å/pix.
x 180 pix.
= 349.2 Å		1.94 Å/pix.
x 180 pix.
= 349.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.772644 - 2.3047986
Average (Standard dev.)0.017896565 (±0.15731609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 349.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54584_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_54584_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 : TPLATE complex

EntireName: TPLATE complex
Components
  • Complex: TPLATE complex

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Supramolecule #1: TPLATE complex

SupramoleculeName: TPLATE complex / type: complex / ID: 1 / Parent: 0
Details: The octameric complex was purified from Arabidopsis thaliana PSB-D cell cultures
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 910 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.14 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
250.0 mMNaClSodium chloride
30.0 mMC6H14N4O2L-arginine
0.5 mMC9H15O6PTCEP
StainingType: NEGATIVE / Material: Uranyl Acetate / Details: A 2% uranyl acetate solution was used for staining
GridModel: EMS Formvar Carbon / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: FORMVAR / Support film - #0 - topology: CONTINUOUS / Support film - #0 - Film thickness: 10 / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.

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Electron microscopy

MicroscopeJEOL 1400
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 2 / Number real images: 1728 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 156991
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)

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