|Entry||Database: EMDB / ID: 8860|
|Title||Cryo-EM structure of the T2SS secretin XcpQ from Pseudomonas aeruginosa|
|Map data||T2SS secretin XcpQ from Pseudomonas aeruginosa|
|Sample||Type 2 secretion system outer membrane secretin XcpQType II secretion system|
|Function / homology||Type II secretion system GspD, conserved site / GspD/PilQ family / Type II/III secretion system / NolW-like / Type II secretion system GspD / NolW-like superfamily / Bacterial type II and III secretion system protein / Bacterial type II/III secretion system short domain / Bacterial type II secretion system protein D signature. / type II protein secretion system complex ...Type II secretion system GspD, conserved site / GspD/PilQ family / Type II/III secretion system / NolW-like / Type II secretion system GspD / NolW-like superfamily / Bacterial type II and III secretion system protein / Bacterial type II/III secretion system short domain / Bacterial type II secretion system protein D signature. / type II protein secretion system complex / protein secretion by the type II secretion system / protein transporter activity / cell outer membrane / identical protein binding / Type II secretion system protein D|
Function and homology information
|Source||Pseudomonas aeruginosa PAO1 (bacteria) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)|
|Method||single particle reconstruction / cryo EM / 3.57 Å resolution|
|Authors||Hay ID / Belousoff MJ / Lithgow TJ|
|Citation||Journal: MBio / Year: 2017|
Title: Structural Basis of Type 2 Secretion System Engagement between the Inner and Outer Bacterial Membranes.
Authors: Iain D Hay / Matthew J Belousoff / Trevor Lithgow
Abstract: Sophisticated nanomachines are used by bacteria for protein secretion. In Gram-negative bacteria, the type 2 secretion system (T2SS) is composed of a pseudopilus assembly platform in the inner ...Sophisticated nanomachines are used by bacteria for protein secretion. In Gram-negative bacteria, the type 2 secretion system (T2SS) is composed of a pseudopilus assembly platform in the inner membrane and a secretin complex in the outer membrane. The engagement of these two megadalton-sized complexes is required in order to secrete toxins, effectors, and hydrolytic enzymes. has at least two T2SSs, with the ancestral nanomachine having a secretin complex composed of XcpQ. Until now, no high-resolution structural information was available to distinguish the features of this -type secretin, which varies greatly in sequence from the well-characterized -type and -type secretins. We have purified the ~1-MDa secretin complex and analyzed it by cryo-electron microscopy. Structural comparisons with the -type secretin complex revealed a striking structural homology despite the differences in their sequence characteristics. At 3.6-Å resolution, the secretin complex was found to have 15-fold symmetry throughout the membrane-embedded region and through most of the domains in the periplasm. However, the N1 domain and N0 domain were not well ordered into this 15-fold symmetry. We suggest a model wherein this disordering of the subunit symmetry for the periplasmic N domains provides a means to engage with the 6-fold symmetry in the inner membrane platform, with a metastable engagement that can be disrupted by substrate proteins binding to the region between XcpP, in the assembly platform, and the XcpQ secretin. How the outer membrane and inner membrane components of the T2SS engage each other and yet can allow for substrate uptake into the secretin chamber has challenged the protein transport field for some time. This vexing question is of significance because the T2SS collects folded protein substrates in the periplasm for transport out of the bacterium and yet must discriminate these few substrate proteins from all the other hundred or so folded proteins in the periplasm. The structural analysis here supports a model wherein substrates must compete against a metastable interaction between XcpP in the assembly platform and the XcpQ secretin, wherein only structurally encoded features in the T2SS substrates compete well enough to disrupt XcpQ-XcpP for entry into the XcpQ chamber, for secretion across the outer membrane.
|Validation Report||PDB-ID: 5wln|
SummaryFull reportAbout validation report
|Date||Deposition: Jul 27, 2017 / Header (metadata) release: Oct 18, 2017 / Map release: Oct 25, 2017 / Last update: Jul 18, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_8860.map.gz (map file in CCP4 format, 136049 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.06 Å|
CCP4 map header:
-Entire Type 2 secretion system outer membrane secretin XcpQ
|Entire||Name: Type 2 secretion system outer membrane secretin XcpQ / Number of components: 2|
-Component #1: protein, Type 2 secretion system outer membrane secretin XcpQ
|Protein||Name: Type 2 secretion system outer membrane secretin XcpQType II secretion system|
Recombinant expression: No
|Mass||Theoretical: 1000 kDa|
|Source||Species: Pseudomonas aeruginosa PAO1 (bacteria)|
|Source (engineered)||Expression System: Escherichia coli (E. coli) / Vector: pET20b / Strain: C43|
-Component #2: protein, Type II secretion system protein D
|Protein||Name: Type II secretion system protein DType II secretion system|
Number of Copies: 15 / Recombinant expression: No
|Mass||Theoretical: 66.485656 kDa|
|Source||Species: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)|
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.5 mg/ml / pH: 8|
|Vitrification||Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 130000. X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
-Atomic model buiding
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi