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 4AV2 | pdb_00004av2

Single particle electron microscopy of PilQ dodecameric complexes from Neisseria meningitidis.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 26.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 4AV2

This is version 1.2 of the entry. See complete history. 

Literature

Structure and Assembly of a Trans-Periplasmic Channel for Type Iv Pili in Neisseria Meningitidis.

Berry, J.L., Phelan, M.M., Collins, R.F., Adomavicius, T., Tonjum, T., Frye, S.A., Bird, L., Owens, R., Ford, R.C., Lian, L.Y., Derrick, J.P.

(2012) PLoS Pathog 8: 2923

  • DOI: https://doi.org/10.1371/journal.ppat.1002923
  • Primary Citation Related Structures: 
    4AQZ, 4AR0, 4AV2

  • PubMed Abstract: 

    Type IV pili are polymeric fibers which protrude from the cell surface and play a critical role in adhesion and invasion by pathogenic bacteria. The secretion of pili across the periplasm and outer membrane is mediated by a specialized secretin protein, PilQ, but the way in which this large channel is formed is unknown. Using NMR, we derived the structures of the periplasmic domains from N. meningitidis PilQ: the N-terminus is shown to consist of two β-domains, which are unique to the type IV pilus-dependent secretins. The structure of the second β-domain revealed an eight-stranded β-sandwich structure which is a novel variant of the HSP20-like fold. The central part of PilQ consists of two α/β fold domains: the structure of the first of these is similar to domains from other secretins, but with an additional α-helix which links it to the second α/β domain. We also determined the structure of the entire PilQ dodecamer by cryoelectron microscopy: it forms a cage-like structure, enclosing a cavity which is approximately 55 Å in internal diameter at its largest extent. Specific regions were identified in the density map which corresponded to the individual PilQ domains: this allowed us to dock them into the cryoelectron microscopy density map, and hence reconstruct the entire PilQ assembly which spans the periplasm. We also show that the C-terminal domain from the lipoprotein PilP, which is essential for pilus assembly, binds specifically to the first α/β domain in PilQ and use NMR chemical shift mapping to generate a model for the PilP:PilQ complex. We conclude that passage of the pilus fiber requires disassembly of both the membrane-spanning and the β-domain regions in PilQ, and that PilP plays an important role in stabilising the PilQ assembly during secretion, through its anchorage in the inner membrane.


  • Organizational Affiliation: 
    • Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 1,202.61 kDa 
  • Atom Count: 33,552 
  • Modeled Residue Count: 4,284 
  • Deposited Residue Count: 11,112 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
745Neisseria meningitidis MC58Mutation(s): 1 
UniProt
Find proteins for Q70M91 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58))
Explore Q70M91 
Go to UniProtKB:  Q70M91
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70M91
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PILP PROTEIN
M, N, O, P, Q
M, N, O, P, Q, R, S, T, U, V, W, X
181Neisseria meningitidis MC58Mutation(s): 0 
UniProt
Find proteins for Q7DD77 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58))
Explore Q7DD77 
Go to UniProtKB:  Q7DD77
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DD77
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 26.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references