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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 / homology: / Prokaryotic 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: To Be Published
Title: CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus
Authors: Gold, V.A.M. / Neuhaus, A. / Gaines, M. / Isupov, M. / McLaren, M.
History
DepositionOct 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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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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