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- PDB-7abk: Helical structure of PspA -

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Basic information

Entry
Database: PDB / ID: 7abk
TitleHelical structure of PspA
ComponentsChloroplast membrane-associated 30 kD protein
KeywordsLIPID BINDING PROTEIN / PspA / IM30 / Vipp1 / ESCRT-III / helical reconstruction / Cryo-EM / membrane remodeling
Function / homologyPspA/IM30 / PspA/IM30 family / Chloroplast membrane-associated 30 kD protein
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsJunglas, B. / Huber, S.T. / Mann, D. / Heidler, T. / Clarke, M. / Schneider, D. / Sachse, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Union (EU)653706 Germany
CitationJournal: Cell / Year: 2021
Title: PspA adopts an ESCRT-III-like fold and remodels bacterial membranes.
Authors: Benedikt Junglas / Stefan T Huber / Thomas Heidler / Lukas Schlösser / Daniel Mann / Raoul Hennig / Mairi Clarke / Nadja Hellmann / Dirk Schneider / Carsten Sachse /
Abstract: PspA is the main effector of the phage shock protein (Psp) system and preserves the bacterial inner membrane integrity and function. Here, we present the 3.6 Å resolution cryoelectron microscopy ...PspA is the main effector of the phage shock protein (Psp) system and preserves the bacterial inner membrane integrity and function. Here, we present the 3.6 Å resolution cryoelectron microscopy (cryo-EM) structure of PspA assembled in helical rods. PspA monomers adopt a canonical ESCRT-III fold in an extended open conformation. PspA rods are capable of enclosing lipids and generating positive membrane curvature. Using cryo-EM, we visualized how PspA remodels membrane vesicles into μm-sized structures and how it mediates the formation of internalized vesicular structures. Hotspots of these activities are zones derived from PspA assemblies, serving as lipid transfer platforms and linking previously separated lipid structures. These membrane fusion and fission activities are in line with the described functional properties of bacterial PspA/IM30/LiaH proteins. Our structural and functional analyses reveal that bacterial PspA belongs to the evolutionary ancestry of ESCRT-III proteins involved in membrane remodeling.
History
DepositionSep 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Chloroplast membrane-associated 30 kD protein


Theoretical massNumber of molelcules
Total (without water)28,2611
Polymers28,2611
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16400 Å2
MethodPISA

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Components

#1: Protein Chloroplast membrane-associated 30 kD protein


Mass: 28260.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: im30 / Plasmid: pRSET6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P74717

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical filament assembly of PspA / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.025 MDa / Experimental value: NO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pRSET6
Buffer solutionpH: 7.6
Buffer componentConc.: 10 mM / Name: Sodium Phosphate / Formula: NaH2PO4
SpecimenConc.: 7.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Pelco easiGlow / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283.15 K / Details: Quantifoil R1.2/1.3 Cu200 grids

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 100000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4CTF correction
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.16-3549model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 35.32 ° / Axial rise/subunit: 2.94 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 5604
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19900 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047950
ELECTRON MICROSCOPYf_angle_d0.52810670
ELECTRON MICROSCOPYf_dihedral_angle_d8.3645065
ELECTRON MICROSCOPYf_chiral_restr0.0311180
ELECTRON MICROSCOPYf_plane_restr0.0031420

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