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- EMDB-0134: Structural snapshots of the Type 9 protein translocon Plug-complex -

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Basic information

Entry
Database: EMDB / ID: 0134
TitleStructural snapshots of the Type 9 protein translocon Plug-complex
Map dataSprA-PPI-Plug complex
SampleComplex of SprA, PPI and Plug
  • Protein involved in gliding motility SprA
  • Peptidyl-prolyl cis-trans isomeraseProlyl isomerase
  • Plug
Function / homologyFKBP-type peptidyl-prolyl cis-trans isomerase domain / Gliding motility protein SprA N-terminal domain / Cell surface SprA / Protein of unknown function DUF5103 / FKBP-type peptidyl-prolyl cis-trans isomerase / Motility related/secretion protein / Domain of unknown function (DUF5103) / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity ...FKBP-type peptidyl-prolyl cis-trans isomerase domain / Gliding motility protein SprA N-terminal domain / Cell surface SprA / Protein of unknown function DUF5103 / FKBP-type peptidyl-prolyl cis-trans isomerase / Motility related/secretion protein / Domain of unknown function (DUF5103) / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Protein involved in gliding motility SprA / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein
Function and homology information
SourceFlavobacterium johnsoniae (bacteria) / Cytophaga johnsonae (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsDeme JC / Lea SM
CitationJournal: Nature / Year: 2018
Title: Type 9 secretion system structures reveal a new protein transport mechanism
Authors: Lauber F / Deme JC / Lea SM / Berks BC
Validation ReportPDB-ID: 6h3j

SummaryFull reportAbout validation report
DateDeposition: Jul 18, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Nov 7, 2018 / Last update: Nov 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0874
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0874
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6h3j
  • Surface level: 0.0874
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0134.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
0.82 Å/pix.
= 246. Å
300 pix
0.82 Å/pix.
= 246. Å
300 pix
0.82 Å/pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density
Contour Level:0.0874 (by author), 0.0874 (movie #1):
Minimum - Maximum-0.10104418 - 0.25124836
Average (Standard dev.)0.0015906628 (0.0132062575)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 246.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z246.000246.000246.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1010.2510.002

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Supplemental data

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Sample components

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Entire Complex of SprA, PPI and Plug

EntireName: Complex of SprA, PPI and Plug / Number of components: 4

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Component #1: protein, Complex of SprA, PPI and Plug

ProteinName: Complex of SprA, PPI and Plug / Recombinant expression: No
MassTheoretical: 335 kDa
SourceSpecies: Flavobacterium johnsoniae (bacteria)

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Component #2: protein, Protein involved in gliding motility SprA

ProteinName: Protein involved in gliding motility SprA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 270.251719 kDa
SourceSpecies: Cytophaga johnsonae (bacteria)

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Component #3: protein, Peptidyl-prolyl cis-trans isomerase

ProteinName: Peptidyl-prolyl cis-trans isomeraseProlyl isomerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.219141 kDa
SourceSpecies: Cytophaga johnsonae (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101

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Component #4: protein, Plug

ProteinName: Plug / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.602969 kDa
SourceSpecies: Cytophaga johnsonae (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 52 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 150000
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Correlation / Refinement space: REAL
Output model

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