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- PDB-8qqj: CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 8qqj
TitleCryoEM structure of the type IV pilin PilA5 from Thermus thermophilus
ComponentsType IV narrow pilus major component PilA5
KeywordsPROTEIN FIBRIL / Type IV pilin glycosylation / twitching motility
Function / homologyProkaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / cell outer membrane / periplasmic space / plasma membrane / Type IV narrow pilus major component PilA5
Function and homology information
Biological speciesThermus thermophilus HB27 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsGold, V.A.M. / Neuhaus, A. / Gaines, M. / Isupov, M. / McLaren, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R008639/1 United Kingdom
CitationJournal: Commun Biol / Year: 2026
Title: Structural insights into the Thermus thermophilus type IV pilus machinery assembling two distinct pili.
Authors: Alexander Neuhaus / Mathew McLaren / Michail N Isupov / Matthew Gaines / Emma Buzzard / Mateusz Sikora / Cyril Hanus / Bertram Daum / Beate Averhoff / Vicki A M Gold /
Abstract: Type IV pili are long, filamentous structures that extend from bacterial cell surfaces, enabling cells to respond to changing environments and facilitating genome plasticity. Thermus thermophilus ...Type IV pili are long, filamentous structures that extend from bacterial cell surfaces, enabling cells to respond to changing environments and facilitating genome plasticity. Thermus thermophilus HB27 produces two different type IV pili, each exhibiting distinct structural and functional properties. Here, we combine cryo-electron tomography, mutagenesis, and AlphaFold predictions to generate hypothetical in situ models of the T. thermophilus type IV pilus assembly machinery. Using single-particle cryo-electron microscopy, we determine structures of both filament types, enabling modelling of their surface glycans. Molecular dynamics simulations further reveal the flexibility of these glycans on extrusion. Integration of the filament structures with our hypothetical model of the assembly machinery offers a framework for further dissecting T4P architecture and biogenesis.
History
DepositionOct 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: Type IV narrow pilus major component PilA5
A: Type IV narrow pilus major component PilA5
B: Type IV narrow pilus major component PilA5
C: Type IV narrow pilus major component PilA5
D: Type IV narrow pilus major component PilA5
E: Type IV narrow pilus major component PilA5
F: Type IV narrow pilus major component PilA5
G: Type IV narrow pilus major component PilA5
H: Type IV narrow pilus major component PilA5
I: Type IV narrow pilus major component PilA5
K: Type IV narrow pilus major component PilA5
L: Type IV narrow pilus major component PilA5
M: Type IV narrow pilus major component PilA5
N: Type IV narrow pilus major component PilA5
O: Type IV narrow pilus major component PilA5
P: Type IV narrow pilus major component PilA5
Q: Type IV narrow pilus major component PilA5
R: Type IV narrow pilus major component PilA5
S: Type IV narrow pilus major component PilA5
T: Type IV narrow pilus major component PilA5
U: Type IV narrow pilus major component PilA5
V: Type IV narrow pilus major component PilA5
W: Type IV narrow pilus major component PilA5
X: Type IV narrow pilus major component PilA5
Y: Type IV narrow pilus major component PilA5
Z: Type IV narrow pilus major component PilA5
a: Type IV narrow pilus major component PilA5
b: Type IV narrow pilus major component PilA5
c: Type IV narrow pilus major component PilA5
d: Type IV narrow pilus major component PilA5
e: Type IV narrow pilus major component PilA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,40793
Polymers354,69631
Non-polymers28,71162
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Type IV narrow pilus major component PilA5 / Type IV major pilin PilA5


Mass: 11441.797 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / References: UniProt: Q72GL2
#2: Polysaccharide...
7-Acetamido-5-acetimidoyl-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic aci-(1-4)-alpha-D- ...7-Acetamido-5-acetimidoyl-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic aci-(1-4)-alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 901.864 Da / Num. of mol.: 31 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2112h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5][Aad22111m-2b_2-6_5*NCC/3=N_7*NCC/3=O]/1-1-2-3/a3-b1_b3-c1_c4-d2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][a-D-GalpNAc]{[(3+1)][a-D-Manp]{[(4+2)]{}}}}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Thermus thermophilus wide pilus / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)
Buffer solutionpH: 8
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 FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 47.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2455
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
9ISOLDEmodel fitting
11PHENIX1.20.1_4487:model refinement
13cryoSPARCfinal Euler assignment
15cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 84 ° / Axial rise/subunit: 11.25 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 2763060
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 475441 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00427001
ELECTRON MICROSCOPYf_angle_d0.81437014
ELECTRON MICROSCOPYf_dihedral_angle_d15.0154774
ELECTRON MICROSCOPYf_chiral_restr0.0485115
ELECTRON MICROSCOPYf_plane_restr0.0044557

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