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- PDB-8gl8: The Type 9 Secretion System Extended Translocon - SprA-PorV-PPI-R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gl8 | |||||||||||||||||||||
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Title | The Type 9 Secretion System Extended Translocon - SprA-PorV-PPI-RemZ-SkpA-SprE complex | |||||||||||||||||||||
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![]() | MEMBRANE PROTEIN / T9SS / Type IX Secretion System Translocon / Protein Secretion PorV - SprA - PPI - RemZ Complex | |||||||||||||||||||||
Function / homology | ![]() peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||||||||||||||
![]() | Deme, J.C. / Lea, S.M. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 922.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 957 KB | Display | ![]() |
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Full document | ![]() | 1010.9 KB | Display | |
Data in XML | ![]() | 100.9 KB | Display | |
Data in CIF | ![]() | 161.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 40194MC ![]() 8gl6C ![]() 8gljC ![]() 8glkC ![]() 8glmC ![]() 8glnC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 6 types, 8 molecules ABFDGCEI
#1: Protein | Mass: 270221.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
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#2: Protein | Mass: 19219.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#3: Protein | Mass: 44210.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#4: Protein | Mass: 113146.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#5: Protein | Mass: 39643.730 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | | Mass: 101274.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 1 types, 6 molecules ![](data/chem/img/MAN.gif)
#8: Sugar | ChemComp-MAN / |
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-Non-polymers , 2 types, 1088 molecules ![](data/chem/img/LMN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-LMN / |
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#9: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Type 9 Secretion System Extended Translocon / Type: COMPLEX / Details: SkpA-SprE-Nterm SprA part of complex / Entity ID: #1-#6 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm |
Image recording | Electron dose: 61.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 546490 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.76 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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