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- EMDB-11698: Helical structure of PspA -

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Basic information

Entry
Database: EMDB / ID: EMD-11698
TitleHelical structure of PspA
Map datasharpened map from phenix.auto_sharpen
Sample
  • Organelle or cellular component: Helical filament assembly of PspA
    • Protein or peptide: Chloroplast membrane-associated 30 kD protein
KeywordsPspA / IM30 / Vipp1 / ESCRT-III / helical reconstruction / Cryo-EM / membrane remodeling / LIPID BINDING PROTEIN
Function / homologyPspA/IM30 / PspA/IM30 family / Chloroplast membrane-associated 30 kD protein
Function and homology information
Biological speciesSynechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsJunglas B / Huber ST
Funding support Germany, 1 items
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, 2020-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7abk
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7abk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11698.png

Downloads & links

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Map

FileDownload / File: emd_11698.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map from phenix.auto_sharpen
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 450 pix.
= 377.505 Å		0.84 Å/pix.
x 450 pix.
= 377.505 Å		0.84 Å/pix.
x 450 pix.
= 377.505 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8389 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-13.684321000000001 - 25.776250000000001
Average (Standard dev.)0.000000000002087 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 377.505 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.83890.83890.8389
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z377.505377.505377.505
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-13.68425.7760.000

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Supplemental data

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Mask #1

Fileemd_11698_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: Guinier sharpened filtered map from Relion Refine3D

Fileemd_11698_additional_1.map
AnnotationGuinier sharpened filtered map from Relion Refine3D
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: unfiltered unsharpened half map from Relion Refine3D

Fileemd_11698_half_map_1.map
Annotationunfiltered unsharpened half map from Relion Refine3D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered unsharpened half map from Relion Refine3D

Fileemd_11698_half_map_2.map
Annotationunfiltered unsharpened half map from Relion Refine3D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

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Sample components

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Entire : Helical filament assembly of PspA

EntireName: Helical filament assembly of PspA
Components
  • Organelle or cellular component: Helical filament assembly of PspA
    • Protein or peptide: Chloroplast membrane-associated 30 kD protein

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Supramolecule #1: Helical filament assembly of PspA

SupramoleculeName: Helical filament assembly of PspA / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Molecular weightTheoretical: 25 KDa

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 28.260816 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGHHHHHHHH HSSGHIDDDD KHMELFNRVG RVLKSQLTHW QQQQEAPEDL LERLLGEMEL ELIELRRALA QTIATFKSTE RQRDAQQLI AQRWYEKAQA ALDRGNEQLA REALGQRQSY QSHTEALGKS LGEQRALVEQ VRGQLQKLER KYLELKSQKN L YLARLKSA ...String:
MGHHHHHHHH HSSGHIDDDD KHMELFNRVG RVLKSQLTHW QQQQEAPEDL LERLLGEMEL ELIELRRALA QTIATFKSTE RQRDAQQLI AQRWYEKAQA ALDRGNEQLA REALGQRQSY QSHTEALGKS LGEQRALVEQ VRGQLQKLER KYLELKSQKN L YLARLKSA IAAQKIEEIA GNLDNASASS LFERIETKIL ELEAERELLN PPPSPLDKKF EQWEEQQAVE ATLAAMKARR SL PPPSS

UniProtKB: Chloroplast membrane-associated 30 kD protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration7.9 mg/mL
BufferpH: 7.6 / Component - Concentration: 10.0 mM / Component - Formula: NaH2PO4 / Component - Name: Sodium Phosphate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Details: Pelco easiGlow
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV / Details: Quantifoil R1.2/1.3 Cu200 grids.

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Electron microscopy

MicroscopeTFS TALOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.94 Å
Applied symmetry - Helical parameters - Δ&Phi: 35.32 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 19900
Segment selectionNumber selected: 5604
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7abk:
Helical structure of PspA

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