[English] 日本語
Yorodumi
- PDB-5wln: Cryo-EM structure of the T2SS secretin XcpQ from Pseudomonas aeru... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5wln
TitleCryo-EM structure of the T2SS secretin XcpQ from Pseudomonas aeruginosa
ComponentsType II secretion system protein DType II secretion system
KeywordsMEMBRANE PROTEIN / T2SS / Secretin / Type 2 secretion system / Pentadecamer / GspD / XcpQ
Function / homologyType 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
Specimen sourcePseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.57 Å resolution
AuthorsHay, I.D. / Belousoff, M.J. / Lithgow, T.J.
CitationJournal: 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
SummaryFull reportAbout validation report
DateDeposition: Jul 27, 2017 / Release: Oct 25, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2017Structure modelrepositoryInitial release
1.1Nov 1, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Jul 18, 2018Structure modelData collection / Experimental preparationem_imaging_optics / em_sample_support_em_imaging_optics.energyfilter_name / _em_sample_support.grid_type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8860
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Type II secretion system protein D
O: Type II secretion system protein D
A: Type II secretion system protein D
B: Type II secretion system protein D
C: Type II secretion system protein D
D: Type II secretion system protein D
E: Type II secretion system protein D
F: Type II secretion system protein D
H: Type II secretion system protein D
I: Type II secretion system protein D
J: Type II secretion system protein D
K: Type II secretion system protein D
L: Type II secretion system protein D
M: Type II secretion system protein D
N: Type II secretion system protein D


Theoretical massNumber of molelcules
Total (without water)997,28515
Polyers997,28515
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein/peptide
Type II secretion system protein D / Type II secretion system / T2SS protein D / General secretion pathway protein D


Mass: 66485.656 Da / Num. of mol.: 15 / Fragment: UNP residues 35-658
Source: (gene. exp.) 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
Gene: xcpQ, PA3105 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P35818

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Type 2 secretion system outer membrane secretin XcpQType II secretion system
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 1 MDa
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pET20b / Strain: C43
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
120 mMHEPES1
2300 mMNaCl1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 130000 / Calibrated defocus min: 600 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF

-
Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4CTF correction
7NAMD2.12model fitting
9PHENIX1.12model refinement
10cryoSPARC0.4.1initial Euler assignment
11cryoSPARC0.4.1final Euler assignment
12cryoSPARC0.4.1classification
13cryoSPARC0.4.13D reconstruction
Image processingDetails: MotionCorr 2.1
CTF correctionDetails: CTFFIND4 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 18005
SymmetryPoint symmetry: C15
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18005 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01252665
ELECTRON MICROSCOPYf_angle_d1.30071475
ELECTRON MICROSCOPYf_dihedral_angle_d7.05932685
ELECTRON MICROSCOPYf_chiral_restr0.0728835
ELECTRON MICROSCOPYf_plane_restr0.0099345

+
About Yorodumi

-
News

-
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.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more

-
Yorodumi

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

Read more