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- PDB-8gl8: The Type 9 Secretion System Extended Translocon - SprA-PorV-PPI-R... -

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Basic information

Entry
Database: PDB / ID: 8gl8
TitleThe Type 9 Secretion System Extended Translocon - SprA-PorV-PPI-RemZ-SkpA-SprE complex
Components
  • Peptidyl-prolyl cis-trans isomerase
  • Periplasmic chaperone for outer membrane proteins Skp
  • Protein involved in gliding motility SprA
  • RemZ
  • SprE
  • Type IX secretion system protein PorV domain-containing protein
KeywordsMEMBRANE PROTEIN / T9SS / Type IX Secretion System Translocon / Protein Secretion PorV - SprA - PPI - RemZ Complex
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / protein stabilization / cytosol
Similarity search - Function
Chaperone protein Skp / Skp domain superfamily / Outer membrane protein (OmpH-like) / Outer membrane protein (OmpH-like) / Type IX secretion system protein PorV / : / Type IX secretion system protein PorV / Gliding motility protein SprA N-terminal domain / Cell surface SprA / Motility related/secretion protein ...Chaperone protein Skp / Skp domain superfamily / Outer membrane protein (OmpH-like) / Outer membrane protein (OmpH-like) / Type IX secretion system protein PorV / : / Type IX secretion system protein PorV / Gliding motility protein SprA N-terminal domain / Cell surface SprA / Motility related/secretion protein / Peptidyl-prolyl cis-trans isomerase FKBP2/11 / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Periplasmic chaperone for outer membrane proteins Skp / Protein involved in gliding motility SprA / SprE / Peptidyl-prolyl cis-trans isomerase / Type IX secretion system protein PorV domain-containing protein / T9SS sorting signal type C domain-containing protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsDeme, J.C. / Lea, S.M.
Funding support United Kingdom, European Union, United States, 6items
OrganizationGrant numberCountry
Wellcome Trust219477/Z/19/Z United Kingdom
Wellcome Trust107929/Z/15/Z United Kingdom
European Research Council (ERC)833713European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007474/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S021264/1 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
CitationJournal: Nat Microbiol / Year: 2024
Title: The Type 9 Secretion System caught in the act of transport
Authors: Lauber, F. / Deme, J.C. / Liu, X. / Kjaer, A. / Miller, H.L. / Alcock, F. / Lea, S.M. / Berks, B.C.
History
DepositionMar 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein involved in gliding motility SprA
B: Peptidyl-prolyl cis-trans isomerase
F: Type IX secretion system protein PorV domain-containing protein
D: RemZ
G: Periplasmic chaperone for outer membrane proteins Skp
C: Periplasmic chaperone for outer membrane proteins Skp
E: Periplasmic chaperone for outer membrane proteins Skp
I: SprE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)669,08915
Polymers667,0038
Non-polymers2,0867
Water19,5821087
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 8 molecules ABFDGCEI

#1: Protein Protein involved in gliding motility SprA


Mass: 270221.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5G5I4
#2: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 19219.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A5F9W9
#3: Protein Type IX secretion system protein PorV domain-containing protein


Mass: 44210.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FJM7
#4: Protein RemZ


Mass: 113146.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FLT3
#5: Protein Periplasmic chaperone for outer membrane proteins Skp


Mass: 39643.730 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5G3C1
#6: Protein SprE


Mass: 101274.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A1E5T9

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Sugars , 1 types, 6 molecules

#8: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 1088 molecules

#7: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1087 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Type 9 Secretion System Extended Translocon / Type: COMPLEX / Details: SkpA-SprE-Nterm SprA part of complex / Entity ID: #1-#6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Buffer solutionpH: 8
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 61.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_4742refinement
PHENIXdev_4742refinement
EM software
IDNameVersionCategory
1SIMPLE3particle selection
4SIMPLE3CTF correction
9RELION3initial Euler assignment
10RELION3final Euler assignment
12RELION33D reconstruction
19PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 546490 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 41.76 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002732833
ELECTRON MICROSCOPYf_angle_d0.526544400
ELECTRON MICROSCOPYf_chiral_restr0.04254821
ELECTRON MICROSCOPYf_plane_restr0.00345825
ELECTRON MICROSCOPYf_dihedral_angle_d5.02794472

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