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- PDB-6h3j: Structural snapshots of the Type 9 protein translocon Plug-complex -

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Basic information

Entry
Database: PDB / ID: 6h3j
TitleStructural snapshots of the Type 9 protein translocon Plug-complex
Components
  • Peptidyl-prolyl cis-trans isomeraseProlyl isomerase
  • Plug
  • Protein involved in gliding motility SprA
KeywordsPROTEIN TRANSPORT / Type 9 Secretion System Type IX Secretion System T9S folded protein secretion outer membrane protein
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
Specimen sourceFlavobacterium johnsoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsDeme, J.C. / Lea, S.M.
CitationJournal: Nature / Year: 2018
Title: Type 9 secretion system structures reveal a new protein transport mechanism
Authors: Lauber, F. / Deme, J.C. / Lea, S.M. / Berks, B.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 18, 2018 / Release: Nov 7, 2018

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Structure visualization

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Assembly

Deposited unit
A: Protein involved in gliding motility SprA
B: Peptidyl-prolyl cis-trans isomerase
C: Plug


Theoretical massNumber of molelcules
Total (without water)338,0743
Polyers338,0743
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)10460
ΔGint (kcal/M)-3
Surface area (Å2)100940
MethodPISA

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Components

#1: Protein/peptide Protein involved in gliding motility SprA


Mass: 270251.719 Da / Num. of mol.: 1 / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5G5I4
#2: Protein/peptide Peptidyl-prolyl cis-trans isomerase / Prolyl isomerase


Mass: 19219.141 Da / Num. of mol.: 1 / Source: (natural) Flavobacterium johnsoniae (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101 / References: UniProt: A5F9W9, peptidylprolyl isomerase
#3: Protein/peptide Plug


Mass: 48602.969 Da / Num. of mol.: 1 / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FJ36

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of SprA, PPI and Plug / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: NATURAL
Molecular weightValue: 0.335 MDa / Experimental value: NO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1SIMPLE2particle selection
4SIMPLE2CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION2.0initial Euler assignment
11RELION2.0final Euler assignment
13RELION2.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 1100000
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 150000 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingRef protocol: BACKBONE TRACE / Ref space: REAL / Target criteria: Correlation

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