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- EMDB-15492: 235 A SynPspA rod after incubation with ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-15492
Title235 A SynPspA rod after incubation with ATP
Map data
Sample
  • Complex: Phage shock protein A (PspA)
    • Protein or peptide: Chloroplast membrane-associated 30 kD protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
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: 4.4 Å
AuthorsJunglas B / Hudina E / Schoennenbeck P / Ritter I / Santiago-Schuebel B / Huesgen P / Sachse C
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural plasticity of bacterial ESCRT-III protein PspA in higher-order assemblies.
Authors: Benedikt Junglas / Esther Hudina / Philipp Schönnenbeck / Ilona Ritter / Anja Heddier / Beatrix Santiago-Schübel / Pitter F Huesgen / Dirk Schneider / Carsten Sachse /
Abstract: Eukaryotic members of the endosome sorting complex required for transport-III (ESCRT-III) family have been shown to form diverse higher-order assemblies. The bacterial phage shock protein A (PspA) ...Eukaryotic members of the endosome sorting complex required for transport-III (ESCRT-III) family have been shown to form diverse higher-order assemblies. The bacterial phage shock protein A (PspA) has been identified as a member of the ESCRT-III superfamily, and PspA homo-oligomerizes to form rod-shaped assemblies. As observed for eukaryotic ESCRT-III, PspA forms tubular assemblies of varying diameters. Using electron cryo-electron microscopy, we determined 61 Synechocystis PspA structures and observed in molecular detail how the structural plasticity of PspA rods is mediated by conformational changes at three hinge regions in the monomer and by the fixed and changing molecular contacts between protomers. Moreover, we reduced and increased the structural plasticity of PspA rods by removing the loop connecting helices α3/α4 and the addition of nucleotides, respectively. Based on our analysis of PspA-mediated membrane remodeling, we suggest that the observed mode of structural plasticity is a prerequisite for the biological function of ESCRT-III members.
History
DepositionJul 31, 2022-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15492.png

Downloads & links

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Map

FileDownload / File: emd_15492.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 400 pix.
= 544.8 Å		1.36 Å/pix.
x 400 pix.
= 544.8 Å		1.36 Å/pix.
x 400 pix.
= 544.8 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.362 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.16687828 - 0.5330789
Average (Standard dev.)0.0017442965 (±0.015553729)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 544.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15492_msk_1.map
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Additional map: Local filtered map

Fileemd_15492_additional_1.map
AnnotationLocal filtered map
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Half map: #2

Fileemd_15492_half_map_1.map
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Half map: #1

Fileemd_15492_half_map_2.map
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Sample components

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Entire : Phage shock protein A (PspA)

EntireName: Phage shock protein A (PspA)
Components
  • Complex: Phage shock protein A (PspA)
    • Protein or peptide: Chloroplast membrane-associated 30 kD protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Phage shock protein A (PspA)

SupramoleculeName: Phage shock protein A (PspA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 120.7 kDa/nm

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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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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 60 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 58.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 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: 6.97 Å
Applied symmetry - Helical parameters - Δ&Phi: 28.3 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46597
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7abk

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

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