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- PDB-8glk: The Type 9 Secretion System dGldL peak II, NucA substrate bound c... -

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Basic information

Entry
Database: PDB / ID: 8glk
TitleThe Type 9 Secretion System dGldL peak II, NucA substrate bound complex
Components
  • Endonuclease I
  • Peptidyl-prolyl cis-trans isomerase
  • Protein involved in gliding motility SprA
  • Type IX secretion system protein PorV domain-containing protein
KeywordsMEMBRANE PROTEIN / T9SS / Type IX Secretion System Translocon / Protein Secretion PorV - SprA - PPI - NucA Complex
Function / homology
Function and homology information


: / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / endonuclease activity
Similarity search - Function
Endonuclease I / Endonuclease I / 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 / Lamin tail domain ...Endonuclease I / Endonuclease I / 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 / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / His-Me finger superfamily / 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 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold
Similarity search - Domain/homology
Protein involved in gliding motility SprA / Peptidyl-prolyl cis-trans isomerase / Endonuclease I / Type IX secretion system protein PorV domain-containing protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 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 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.0Jan 31, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 31, 2024Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 31, 2024Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 31, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 31, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 31, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 31, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 31, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 31, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Endonuclease I
A: Protein involved in gliding motility SprA
B: Peptidyl-prolyl cis-trans isomerase
F: Type IX secretion system protein PorV domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,1115
Polymers342,1054
Non-polymers1,0051
Water00
1


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

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Components

#1: Protein Endonuclease I


Mass: 8454.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FAQ0
#2: 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
#3: 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
#4: 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
#5: 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
Has ligand of interestN
Has protein modificationN

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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 NucA complex / Type: COMPLEX / Entity ID: #1-#4 / 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: 62.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1SIMPLE3particle selection
4SIMPLE3CTF correction
8PHENIXmodel refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57573 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00222384
ELECTRON MICROSCOPYf_angle_d0.51330390
ELECTRON MICROSCOPYf_dihedral_angle_d5.2263047
ELECTRON MICROSCOPYf_chiral_restr0.0453303
ELECTRON MICROSCOPYf_plane_restr0.0044024

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