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- PDB-8tj2: CryoEM structure of Myxococcus xanthus type IV pilus -

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Basic information

Entry
Database: PDB / ID: 8tj2
TitleCryoEM structure of Myxococcus xanthus type IV pilus
ComponentsType IV major pilin protein PilA
KeywordsCELL ADHESION / filament / helical reconstruction / CryoEM
Function / homologyType IV pilin PilA / Type IV pilin PilA / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / pilus / membrane / Type IV major pilin protein PilA
Function and homology information
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsZheng, W. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2024
Title: Tight-packing of large pilin subunits provides distinct structural and mechanical properties for the type IVa pilus.
Authors: Anke Treuner-Lange / Weili Zheng / Albertus Viljoen / Steffi Lindow / Marco Herfurth / Yves F Dufrêne / Lotte Søgaard-Andersen / Edward H Egelman /
Abstract: Type IVa pili (T4aP) are ubiquitous cell surface filaments important for surface motility, adhesion to surfaces, DNA uptake, biofilm formation, and virulence. T4aP are built from thousands of copies ...Type IVa pili (T4aP) are ubiquitous cell surface filaments important for surface motility, adhesion to surfaces, DNA uptake, biofilm formation, and virulence. T4aP are built from thousands of copies of the major pilin subunit and tipped by a complex composed of minor pilins and in some systems also the PilY1 adhesin. While major pilins of structurally characterized T4aP have lengths of <165 residues, the major pilin PilA of is unusually large with 208 residues. All major pilins have a conserved N-terminal domain and a variable C-terminal domain, and the additional residues of PilA are due to a larger C-terminal domain. We solved the structure of the T4aP (T4aP) at a resolution of 3.0 Å using cryo-EM. The T4aP follows the structural blueprint of other T4aP with the pilus core comprised of the interacting N-terminal α1-helices, while the globular domains decorate the T4aP surface. The atomic model of PilA built into this map shows that the large C-terminal domain has more extensive intersubunit contacts than major pilins in other T4aP. As expected from these greater contacts, the bending and axial stiffness of the T4aP is significantly higher than that of other T4aP and supports T4aP-dependent motility on surfaces of different stiffnesses. Notably, T4aP variants with interrupted intersubunit interfaces had decreased bending stiffness, pilus length, and strongly reduced motility. These observations support an evolutionary scenario whereby the large major pilin enables the formation of a rigid T4aP that expands the environmental conditions in which the T4aP system functions.
#1: Journal: bioRxiv / Year: 2023
Title: Large pilin subunits provide distinct structural and mechanical properties for the type IV pilus.
Authors: Anke Treuner-Lange / Weili Zheng / Albertus Viljoen / Steffi Lindow / Marco Herfurth / Yves F Dufrêne / Lotte Søgaard-Andersen / Edward H Egelman
Abstract: Type IV pili (T4P) are ubiquitous bacterial cell surface filaments important for surface motility, adhesion to biotic and abiotic surfaces, DNA uptake, biofilm formation, and virulence. T4P are built ...Type IV pili (T4P) are ubiquitous bacterial cell surface filaments important for surface motility, adhesion to biotic and abiotic surfaces, DNA uptake, biofilm formation, and virulence. T4P are built from thousands of copies of the major pilin subunit and tipped by a complex composed of minor pilins and in some systems also the PilY1 adhesin. While the major pilins of structurally characterized T4P have lengths of up to 161 residues, the major pilin PilA of is unusually large with 208 residues. All major pilins have a highly conserved N-terminal domain and a highly variable C-terminal domain, and the additional residues in the PilA are due to a larger C-terminal domain. We solved the structure of the T4P (T4P ) at a resolution of 3.0 Å using cryo-electron microscopy (cryo-EM). The T4P follows the structural blueprint observed in other T4P with the pilus core comprised of the extensively interacting N-terminal α1-helices while the globular domains decorate the T4P surface. The atomic model of PilA built into this map shows that the large C-terminal domain has much more extensive intersubunit contacts than major pilins in other T4P. As expected from these greater contacts, the bending and axial stiffness of the T4P is significantly higher than that of other T4P and supports T4P-dependent motility on surfaces of different stiffnesses. Notably, T4P variants with interrupted intersubunit interfaces had decreased bending stiffness and strongly reduced motility on all surfaces. These observations support an evolutionary scenario whereby the large major pilin enables the formation of a rigid T4P that expands the environmental conditions in which the T4P system functions.
History
DepositionJul 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Type IV major pilin protein PilA
D: Type IV major pilin protein PilA
E: Type IV major pilin protein PilA
F: Type IV major pilin protein PilA
G: Type IV major pilin protein PilA
H: Type IV major pilin protein PilA
I: Type IV major pilin protein PilA
J: Type IV major pilin protein PilA
K: Type IV major pilin protein PilA
A: Type IV major pilin protein PilA
L: Type IV major pilin protein PilA
M: Type IV major pilin protein PilA
N: Type IV major pilin protein PilA
O: Type IV major pilin protein PilA
P: Type IV major pilin protein PilA
Q: Type IV major pilin protein PilA
R: Type IV major pilin protein PilA
S: Type IV major pilin protein PilA


Theoretical massNumber of molelcules
Total (without water)394,78218
Polymers394,78218
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Type IV major pilin protein PilA / Pilin


Mass: 21932.318 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria) / References: UniProt: Q59589

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Myxococcus xanthus type IV pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 100.7 ° / Axial rise/subunit: 10 Å / Axial symmetry: C1
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1300000 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00628404
ELECTRON MICROSCOPYf_angle_d0.70438682
ELECTRON MICROSCOPYf_dihedral_angle_d5.0154014
ELECTRON MICROSCOPYf_chiral_restr0.0454194
ELECTRON MICROSCOPYf_plane_restr0.0065310

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