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- EMDB-13428: Pfu sArlG (PF0333, N-d31-ArlG) -

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Basic information

Entry
Database: EMDB / ID: EMD-13428
TitlePfu sArlG (PF0333, N-d31-ArlG)
Map dataPyrococcus furiosus sArlG Refinement Map
Sample
  • Complex: Homo-oligomeric helical filament of archaellum stator component Pfu sArlG
    • Protein or peptide: Pyrococcus furiosus sArlG
Biological speciesPyrococcus furiosus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsUmrekar TR / Winterborn YB / Sivabalasarma S / Brantl J / Albers SV / Beeby M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Commission686647European Union
CitationJournal: Front Microbiol / Year: 2021
Title: Evolution of Archaellum Rotation Involved Invention of a Stator Complex by Duplicating and Modifying a Core Component.
Authors: Trishant R Umrekar / Yvonne B Winterborn / Shamphavi Sivabalasarma / Julian Brantl / Sonja-Verena Albers / Morgan Beeby /
Abstract: Novelty in biology can arise from opportunistic repurposing of nascent characteristics of existing features. Understanding how this process happens at the molecular scale, however, suffers from a ...Novelty in biology can arise from opportunistic repurposing of nascent characteristics of existing features. Understanding how this process happens at the molecular scale, however, suffers from a lack of case studies. The evolutionary emergence of rotary motors is a particularly clear example of evolution of a new function. The simplest of rotary motors is the archaellum, a molecular motor that spins a helical propeller for archaeal motility analogous to the bacterial flagellum. Curiously, emergence of archaellar rotation may have pivoted on the simple duplication and repurposing of a pre-existing component to produce a stator complex that anchors to the cell superstructure to enable productive rotation of the rotor component. This putative stator complex is composed of ArlF and ArlG, gene duplications of the filament component ArlB, providing an opportunity to study how gene duplication and neofunctionalization contributed to the radical innovation of rotary function. Toward understanding how this happened, we used electron cryomicroscopy to determine the structure of isolated ArlG filaments, the major component of the stator complex. Using a hybrid modeling approach incorporating structure prediction and validation, we show that ArlG filaments are open helices distinct to the closed helical filaments of ArlB. Curiously, further analysis reveals that ArlG retains a subset of the inter-protomer interactions of homologous ArlB, resulting in a superficially different assembly that nevertheless reflects the common ancestry of the two structures. This relatively simple mechanism to change quaternary structure was likely associated with the evolutionary neofunctionalization of the archaellar stator complex, and we speculate that the relative deformable elasticity of an open helix may facilitate elastic energy storage during the transmission of the discrete bursts of energy released by ATP hydrolysis to continuous archaellar rotation, allowing the inherent properties of a duplicated ArlB to be co-opted to fulfill a new role. Furthermore, agreement of diverse experimental evidence in our work supports recent claims to the power of new structure prediction techniques.
History
DepositionAug 19, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateFeb 2, 2022-
Current statusFeb 2, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.48
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.48
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13428.png

Downloads & links

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Map

FileDownload / File: emd_13428.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPyrococcus furiosus sArlG Refinement Map
Voxel sizeX=Y=Z: 1.7 Å
Density
Contour LevelBy AUTHOR: 0.48 / Movie #1: 0.48
Minimum - Maximum-0.36032236 - 1.945895
Average (Standard dev.)0.007573213 (±0.09668549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z255.000255.000255.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.3601.9460.008

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Supplemental data

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Mask #1

Fileemd_13428_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pyrococcus furiosus sArlG half map A

Fileemd_13428_half_map_1.map
AnnotationPyrococcus furiosus sArlG half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pyrococcus furiosus sArlG half map B

Fileemd_13428_half_map_2.map
AnnotationPyrococcus furiosus sArlG half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homo-oligomeric helical filament of archaellum stator component P...

EntireName: Homo-oligomeric helical filament of archaellum stator component Pfu sArlG
Components
  • Complex: Homo-oligomeric helical filament of archaellum stator component Pfu sArlG
    • Protein or peptide: Pyrococcus furiosus sArlG

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Supramolecule #1: Homo-oligomeric helical filament of archaellum stator component P...

SupramoleculeName: Homo-oligomeric helical filament of archaellum stator component Pfu sArlG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pyrococcus furiosus (archaea)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Recombinant plasmid: pSVA4014
Molecular weightTheoretical: 142.4235 KDa

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Macromolecule #1: Pyrococcus furiosus sArlG

MacromoleculeName: Pyrococcus furiosus sArlG / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
TDIANGMKDR GKLLANQLRV EFAIINDPQS VRVTGTGPYT YTFYIKNIGK ETIPFTSSSV QVFIDGNLIP PSNLTFKDVN GNQITSLKPY EVGVLEVTLG NPLDTTTTHR IVVVLENGKK RSLVFRVKS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTris-HCLtris hydrochloride

Details: Solutions were filtered and chilled before use in column chromatography.
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 40.0 sec. / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: cryoSPARC (ver. 3.2), CTFFIND (ver. 4))
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 40178
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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