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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: To Be Published
Title: Non-canonical ATPase activity drives PspA membrane constriction
Authors: Junglas B / Hudina E / Schoennenbeck P / Ritter I / Santiago-Schuebel B / Huesgen P / Sachse C
History
DepositionJul 31, 2022-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 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

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.362 Å
Density

Histogram

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
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Local filtered map

Fileemd_15492_additional_1.map
AnnotationLocal filtered map
Projections & Slices
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Half map: #2

Fileemd_15492_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15492_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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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 / Adenosine diphosphate

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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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7abk

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

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