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- PDB-4av2: Single particle electron microscopy of PilQ dodecameric complexes... -

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Basic information

Entry
Database: PDB / ID: 4av2
TitleSingle particle electron microscopy of PilQ dodecameric complexes from Neisseria meningitidis.
Components
  • PILP PROTEIN
  • TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
KeywordsPROTEIN TRANSPORT / OUTER MEMBRANE PROTEIN / PILUS BIOGENESIS
Function / homology
Function and homology information


establishment of competence for transformation / protein secretion / cell outer membrane
Similarity search - Function
Type IV pilus inner membrane component PilP / Pilus assembly protein, PilP / 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 IV pilus inner membrane component PilP / Pilus assembly protein, PilP / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Type IV pilus biogenesis and competence protein PilQ / PilP protein
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS MC58 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 26 Å
AuthorsBerry, 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.
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
DepositionMay 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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Structure visualization

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  • Deposited structure unit
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  • EMDB-2105
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Structure viewerMolecule:
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Assembly

Deposited unit
A: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
B: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
C: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
D: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
E: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
F: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
G: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
H: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
I: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
J: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
K: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
L: TYPE IV PILUS BIOGENESIS AND COMPETENCE PROTEIN PILQ
M: PILP PROTEIN
N: PILP PROTEIN
O: PILP PROTEIN
P: PILP PROTEIN
Q: PILP PROTEIN
R: PILP PROTEIN
S: PILP PROTEIN
T: PILP PROTEIN
U: PILP PROTEIN
V: PILP PROTEIN
W: PILP PROTEIN
X: PILP PROTEIN


Theoretical massNumber of molelcules
Total (without water)1,202,60924
Polymers1,202,60924
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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


Mass: 80129.922 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) NEISSERIA MENINGITIDIS MC58 (bacteria) / References: UniProt: Q70M91
#2: Protein
PILP PROTEIN


Mass: 20087.498 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) NEISSERIA MENINGITIDIS MC58 (bacteria) / References: UniProt: Q7DD77

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: OUTER MEMBRANE PROTEIN PILQ FROM NEISSERIA MENINGITIDIS
Type: COMPLEX / Details: PILQ ISOLATED IN DETERGENT
Buffer solutionName: 10 MM TRIS-HCL, PH 7.5, 150 MM NACL, 5 MM EDTA, AND 0.1% (W/V) ZWITTERGENT 3-10
pH: 7.5
Details: 10 MM TRIS-HCL, PH 7.5, 150 MM NACL, 5 MM EDTA, AND 0.1% (W/V) ZWITTERGENT 3-10
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 100K, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BOTH SIDES OF THE GRID WERE BRIEFLY BLOTTED DRY WITH WHATMAN NO. 1 FILTER ...Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 100K, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BOTH SIDES OF THE GRID WERE BRIEFLY BLOTTED DRY WITH WHATMAN NO. 1 FILTER PAPER IN A HUMIDITY-CONTROLLED CHAMBER USING A VITROBOT (FEI) DEVICE (90PERCENT RELATIVE HUMIDITY), AND THE GRID WAS THEN PLUNGED INTO LIQUID ETHANE MAINTAINED AT LESS THAN 100K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Nov 27, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 33000 X / Calibrated magnification: 33112 X / Nominal defocus max: 5100 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTemperature: 97 K
Image recordingElectron dose: 4 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 55

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Processing

EM softwareName: EMAN / Category: 3D reconstruction
CTF correctionDetails: CTFFIT EACH MICROGRAPH
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionMethod: EMAN / Resolution: 26 Å / Num. of particles: 25303 / Nominal pixel size: 4.53 Å / Actual pixel size: 4.53 Å / Magnification calibration: 33113
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2105. (DEPOSITION ID: 10821).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Details: METHOD--LOCAL CORRELATION
RefinementHighest resolution: 26 Å
Refinement stepCycle: LAST / Highest resolution: 26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33552 0 0 0 33552

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