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- PDB-8qqd: CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 8qqd
TitleCryoEM structure of the type IV pilin PilA4 from Thermus thermophilus
ComponentsPilA
KeywordsPROTEIN FIBRIL / Type IV pilin glycosylation / twitching motility
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane / periplasmic space
Similarity search - Function
Bacterial general secretion pathway protein G-type pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / PilA
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.4 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
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Description: Ligand geometry / Provider: author / Type: Coordinate replacement
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PilA
B: PilA
C: PilA
D: PilA
E: PilA
F: PilA
G: PilA
H: PilA
I: PilA
J: PilA
K: PilA
L: PilA
M: PilA
N: PilA
O: PilA
P: PilA
Q: PilA
R: PilA
S: PilA
T: PilA
U: PilA
V: PilA
W: PilA
X: PilA
Y: PilA
Z: PilA
a: PilA
b: PilA
c: PilA
d: PilA
e: PilA
f: PilA
g: PilA
h: PilA
i: PilA
j: PilA
k: PilA
l: PilA
m: PilA
n: PilA
o: PilA
p: PilA
q: PilA
r: PilA
s: PilA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)673,233180
Polymers596,30145
Non-polymers76,933135
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 ...
PilA


Mass: 13251.123 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8KPZ0
#2: Polysaccharide...
alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy- ...alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 45
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DGalpNAca1-3DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][a-D-GalpNAc]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 45
Source method: isolated from a genetically manipulated source
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
#4: Sugar...
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 45
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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: TFS 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)
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
9ISOLDEmodel fitting
11REFMAC5model refinement
15cryoSPARC4.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 92.36 ° / Axial rise/subunit: 9.242 Å / Axial symmetry: C1
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 654248 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementResolution: 2.4→2.4 Å / Cor.coef. Fo:Fc: 0.887
RfactorNum. reflection% reflection
Rwork0.41052 --
obs0.41052 0 100 %
Displacement parametersBiso mean: 62.596 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0.01 Å20.01 Å2
2---1.09 Å2-0 Å2
3---2.18 Å2

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