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- PDB-6h3i: Structural snapshots of the Type 9 protein translocon -

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Database: PDB / ID: 6h3i
TitleStructural snapshots of the Type 9 protein translocon
  • Peptidyl-prolyl cis-trans isomeraseProlyl isomerase
  • PorV
  • 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 / FKBP-type peptidyl-prolyl cis-trans isomerase / Motility related/secretion protein / 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 / 3.5 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: Frédéric Lauber / Justin C Deme / Susan M Lea / Ben C Berks
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 18, 2018 / Release: Nov 7, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 7, 2018Structure modelrepositoryInitial release
1.1Nov 21, 2018Structure modelData collection / Database referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.2Dec 12, 2018Structure modelData collection / Database referencescitation_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last

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

Theoretical massNumber of molelcules
Total (without water)333,6513

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)9890
ΔGint (kcal/M)-45
Surface area (Å2)102400


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

Mass: 270221.688 Da / Num. of mol.: 1
Details: SprA from flavobacterium johnsoniae uniprot Q5I6C7 fjoh_1653
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 PorV

Mass: 44210.043 Da / Num. of mol.: 1 / Source: (natural) Flavobacterium johnsoniae (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101 / References: UniProt: A5FJM7

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: Complex of SprA, PPI and PorV / 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

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)


EM software
1SIMPLE2particle selection
4SIMPLE2CTF correction
7Cootmodel fitting
9RELION2.0initial Euler assignment
10RELION2.0final Euler assignment
12RELION2.03D reconstruction
13PHENIXmodel refinement
Particle selectionNumber of particles selected: 1100000
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 210000 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: BACKBONE TRACE / Ref space: REAL / Target criteria: Correlation

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