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- PDB-4aqz: B2 domain of Neisseria meningitidis Pilus assembly protein PilQ -

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Basic information

Entry
Database: PDB / ID: 4aqz
TitleB2 domain of Neisseria meningitidis Pilus assembly protein PilQ
ComponentsTYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
KeywordsTRANSPORT PROTEIN / SECRETIN / TYPE IV PILI / TYPE II SECRETION SYSTEM
Function / homology
Function and homology information


establishment of competence for transformation / protein secretion / cell outer membrane
Similarity search - Function
Immunoglobulin-like - #3470 / Type IV pilus secretin PilQ / AMIN domain / AMIN domain / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site ...Immunoglobulin-like - #3470 / Type IV pilus secretin PilQ / AMIN domain / AMIN domain / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Type IV pilus biogenesis and competence protein PilQ
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodSOLUTION NMR / CYANA2.1, CNS1.2 WATER REFINEMENT
AuthorsPhelan, M.M. / Berry, J.L. / Derrick, J.P. / Lian, L.Y.
CitationJournal: PLoS Pathog / Year: 2012
Title: Structure and assembly of a trans-periplasmic channel for type IV pili in Neisseria meningitidis.
Authors: Jamie-Lee Berry / Marie M Phelan / Richard F Collins / Tomas Adomavicius / Tone Tønjum / Stefan A Frye / Louise Bird / Ray Owens / Robert C Ford / Lu-Yun Lian / Jeremy P Derrick /
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 ...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.
History
DepositionApr 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ


Theoretical massNumber of molelcules
Total (without water)15,1901
Polymers15,1901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ / PILQ


Mass: 15190.270 Da / Num. of mol.: 1 / Fragment: B2, RESIDUES 224-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE21) / References: UniProt: Q70M91

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D HN(CA)CO 3D HNCO
1412D 1H-15N HSQC
1513D HBHA(CO)NH
1613D HBHANH
1713D HN(CA)CB
1812D (HB)CB(CGCD)HD
1912D ALI 1H-13C HSQC
11012D ARO 1H-13C HSQC
11113D ALI HC-NOESY
11213D ARO HC- NOESY
11313D HN-NOESY
11413D ALI (H)CCH-TOCSY
11513D ARO (H)CCH-TOCSY
NMR detailsText: REPRESENTATIVE STRUCTURE SELECTED AS CLOSEST-TO- MEAN FOR THE ENSEMBLE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 100 mM / pH: 6.8 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANALOPEZ ET ALrefinement
TopSpinstructure solution
CcpNmr AnalysisANALYSISstructure solution
CYANAstructure solution
CNSstructure solution
TALOS+structure solution
RefinementMethod: CYANA2.1, CNS1.2 WATER REFINEMENT / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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