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- EMDB-3997: N2 and N3 ring of PilQ from Thermus thermophilus -

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Basic information

Entry
Database: EMDB / ID: EMD-3997
TitleN2 and N3 ring of PilQ from Thermus thermophilus
Map dataNone
Sample
  • Complex: PilQ complex with 13-fold symmetry
Biological speciesThermus thermophilus HB27 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsD'Imprima E / Vonck J / Sanchez R
CitationJournal: Elife / Year: 2017
Title: Cryo-EM structure of the bifunctional secretin complex of .
Authors: Edoardo D'Imprima / Ralf Salzer / Ramachandra M Bhaskara / Ricardo Sánchez / Ilona Rose / Lennart Kirchner / Gerhard Hummer / Werner Kühlbrandt / Janet Vonck / Beate Averhoff /
Abstract: Secretins form multimeric channels across the outer membrane of Gram-negative bacteria that mediate the import or export of substrates and/or extrusion of type IV pili. The secretin complex of is an ...Secretins form multimeric channels across the outer membrane of Gram-negative bacteria that mediate the import or export of substrates and/or extrusion of type IV pili. The secretin complex of is an oligomer of the 757-residue PilQ protein, essential for DNA uptake and pilus extrusion. Here, we present the cryo-EM structure of this bifunctional complex at a resolution of ~7 Å using a new reconstruction protocol. Thirteen protomers form a large periplasmic domain of six stacked rings and a secretin domain in the outer membrane. A homology model of the PilQ protein was fitted into the cryo-EM map. A crown-like structure outside the outer membrane capping the secretin was found not to be part of PilQ. Mutations in the secretin domain disrupted the crown and abolished DNA uptake, suggesting a central role of the crown in natural transformation.
History
DepositionNov 15, 2017-
Header (metadata) releaseDec 13, 2017-
Map releaseJan 10, 2018-
UpdateMar 28, 2018-
Current statusMar 28, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0385
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3997.png

Downloads & links

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Map

FileDownload / File: emd_3997.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 324 pix.
= 528.12 Å		1.63 Å/pix.
x 324 pix.
= 528.12 Å		1.63 Å/pix.
x 324 pix.
= 528.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0385 / Movie #1: 0.0385
Minimum - Maximum-0.041751556 - 0.09502463
Average (Standard dev.)0.000058266138 (±0.0019338897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 528.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z528.120528.120528.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-0.0420.0950.000

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Supplemental data

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Sample components

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Entire : PilQ complex with 13-fold symmetry

EntireName: PilQ complex with 13-fold symmetry
Components
  • Complex: PilQ complex with 13-fold symmetry

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Supramolecule #1: PilQ complex with 13-fold symmetry

SupramoleculeName: PilQ complex with 13-fold symmetry / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)
Molecular weightTheoretical: 1 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blotting for 8-10 seconds.

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Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Lower energy threshold: 18 eV / Energy filter - Upper energy threshold: 18 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-45 / Average exposure time: 9.0 sec. / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30675 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal magnification: 20000
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 11457
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: INSILICO MODEL
In silico model: a featureless cylinder generated in Xmipp 3.1
Final reconstructionApplied symmetry - Point group: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 2646
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN
Details: The images of the subdomain containing the N2 and N3 rings after residual signal subtraction were recentered and placed in a smaller with our new program REP, followed by refinement by FREALIGN.
FSC plot (resolution estimation)

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