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- EMDB-52540: 320 A SynPspA rod after incubation with EPL -

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Basic information

Entry
Database: EMDB / ID: EMD-52540
Title320 A SynPspA rod after incubation with EPL
Map data
Sample
  • Complex: Helical assembly of SynPspA after incubation with EPL
    • Protein or peptide: Chloroplast membrane-associated 30 kD protein
KeywordsNucleotide binding / Helical assembly / ESCRT-III fold / Membrane remodeling / LIPID BINDING PROTEIN
Function / homologyPspA/IM30 / PspA/IM30 family / Chloroplast membrane-associated 30 kD protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsHudina E / Junglas B / Sachse C
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SA 1882/6-1 Germany
German Research Foundation (DFG)SCHN 690/16-1 Germany
German Research Foundation (DFG)SFB1551 Germany
German Research Foundation (DFG)SFB1552 Germany
German Research Foundation (DFG)SFB1208 Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: The bacterial ESCRT-III PspA rods thin lipid tubules and increase membrane curvature through helix α0 interactions.
Authors: Esther Hudina / Stephan Schott-Verdugo / Benedikt Junglas / Mirka Kutzner / Ilona Ritter / Nadja Hellmann / Dirk Schneider / Holger Gohlke / Carsten Sachse /
Abstract: The phage shock protein A (PspA), a bacterial member of the endosomal sorting complexes required for transport (ESCRT)-III superfamily, forms rod-shaped helical assemblies that internalize membrane ...The phage shock protein A (PspA), a bacterial member of the endosomal sorting complexes required for transport (ESCRT)-III superfamily, forms rod-shaped helical assemblies that internalize membrane tubules. The N-terminal helix α0 of PspA (and other ESCRT-III members) has been suggested to act as a membrane anchor; the detailed mechanism, however, of how it binds to membranes and eventually triggers membrane fusion and/or fission events remains unclear. By solving a total of 15 cryoelectron microscopy (cryo-EM) structures of PspA and a truncation lacking the N-terminal helix α0 in the presence of polar lipid membranes, we show in molecular detail how PspA interacts with and remodels membranes: Binding of the N-terminal helix α0 in the outer tubular membrane leaflet induces membrane curvature, supporting membrane tubulation by PspA. Detailed molecular dynamics simulations and free energy computations of interactions between the helix α0 and negatively charged membranes suggest a compensating mechanism between helix-membrane interactions and the energy contributions required for membrane bending. The energetic considerations are in line with the membrane structures observed in the cryo-EM images of tubulated membrane vesicles, fragmented vesicles inside tapered PspA rods, and shedded vesicles emerging at the thinner PspA rod ends. Our results provide insights into the molecular determinants and a potential mechanism of vesicular membrane remodeling mediated by a member of the ESCRT-III superfamily.
History
DepositionJan 14, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52540.png

Downloads & links

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Map

FileDownload / File: emd_52540.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.123856775 - 0.53232473
Average (Standard dev.)0.0016402629 (±0.014865707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52540_half_map_1.map
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Half map: #2

Fileemd_52540_half_map_2.map
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Sample components

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Entire : Helical assembly of SynPspA after incubation with EPL

EntireName: Helical assembly of SynPspA after incubation with EPL
Components
  • Complex: Helical assembly of SynPspA after incubation with EPL
    • Protein or peptide: Chloroplast membrane-associated 30 kD protein

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Supramolecule #1: Helical assembly of SynPspA after incubation with EPL

SupramoleculeName: Helical assembly of SynPspA after incubation with EPL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 1.7 MDa

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Macromolecule #1: Chloroplast membrane-associated 30 kD protein

MacromoleculeName: Chloroplast membrane-associated 30 kD protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 28.097758 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSSAALEVLF QGPMELFNRV GRVLKSQLTH WQQQQEAPED LLERLLGEME LELIELRRAL AQTIATFKST ERQRDAQQL IAQRWYEKAQ AALDRGNEQL AREALGQRQS YQSHTEALGK SLGEQRALVE QVRGQLQKLE RKYLELKSQK N LYLARLKS ...String:
MGSSHHHHHH SSSAALEVLF QGPMELFNRV GRVLKSQLTH WQQQQEAPED LLERLLGEME LELIELRRAL AQTIATFKST ERQRDAQQL IAQRWYEKAQ AALDRGNEQL AREALGQRQS YQSHTEALGK SLGEQRALVE QVRGQLQKLE RKYLELKSQK N LYLARLKS AIAAQKIEEI AGNLDNASAS SLFERIETKI LELEAERELL NPPPSPLDKK FEQWEEQQAV EATLAAMKAR RS LPPPSS

UniProtKB: Chloroplast membrane-associated 30 kD protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.53 Å
Applied symmetry - Helical parameters - Δ&Phi: -140.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69652
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7abk

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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