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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
ComponentsType IV wide pilus major component PilA4
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 / plasma membrane
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 / alpha-D-mannopyranose / Type IV wide pilus major component PilA4
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: 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.
History
DepositionOct 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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
d: Type IV wide pilus major component PilA4
A: Type IV wide pilus major component PilA4
B: Type IV wide pilus major component PilA4
C: Type IV wide pilus major component PilA4
D: Type IV wide pilus major component PilA4
E: Type IV wide pilus major component PilA4
F: Type IV wide pilus major component PilA4
G: Type IV wide pilus major component PilA4
H: Type IV wide pilus major component PilA4
I: Type IV wide pilus major component PilA4
J: Type IV wide pilus major component PilA4
K: Type IV wide pilus major component PilA4
L: Type IV wide pilus major component PilA4
M: Type IV wide pilus major component PilA4
N: Type IV wide pilus major component PilA4
O: Type IV wide pilus major component PilA4
P: Type IV wide pilus major component PilA4
Q: Type IV wide pilus major component PilA4
R: Type IV wide pilus major component PilA4
S: Type IV wide pilus major component PilA4
T: Type IV wide pilus major component PilA4
U: Type IV wide pilus major component PilA4
V: Type IV wide pilus major component PilA4
W: Type IV wide pilus major component PilA4
X: Type IV wide pilus major component PilA4
Y: Type IV wide pilus major component PilA4
Z: Type IV wide pilus major component PilA4
a: Type IV wide pilus major component PilA4
b: Type IV wide pilus major component PilA4
c: Type IV wide pilus major component PilA4
e: Type IV wide pilus major component PilA4
f: Type IV wide pilus major component PilA4
g: Type IV wide pilus major component PilA4
h: Type IV wide pilus major component PilA4
i: Type IV wide pilus major component PilA4
j: Type IV wide pilus major component PilA4
k: Type IV wide pilus major component PilA4
l: Type IV wide pilus major component PilA4
m: Type IV wide pilus major component PilA4
n: Type IV wide pilus major component PilA4
o: Type IV wide pilus major component PilA4
p: Type IV wide pilus major component PilA4
q: Type IV wide pilus major component PilA4
r: Type IV wide pilus major component PilA4
s: Type IV wide pilus major component PilA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)674,044225
Polymers596,30145
Non-polymers77,743180
Water00
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 wide pilus major component PilA4 / Type IV major pilin PilA4


Mass: 13251.123 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72JC0
#2: Polysaccharide...
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 45
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAca1-3DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1a_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][a-D-GalpNAc]{}}}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-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 45
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: 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: 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)
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
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
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00347250
ELECTRON MICROSCOPYf_angle_d0.76464665
ELECTRON MICROSCOPYf_dihedral_angle_d12.9618775
ELECTRON MICROSCOPYf_chiral_restr0.0578775
ELECTRON MICROSCOPYf_plane_restr0.0037695

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