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- PDB-7jsv: Cryo-EM structure of conjugative pili from carbapenem-resistant K... -

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Basic information

Entry
Database: PDB / ID: 7jsv
TitleCryo-EM structure of conjugative pili from carbapenem-resistant Klebsiella pneumoniae
ComponentsPilin
KeywordsPROTEIN FIBRIL / Conjugation pili / Helical reconstruction
Function / homologyTraA / TraA / : / membrane => GO:0016020 / extracellular region / plasma membrane / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Pilin / Pilin
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZheng, W. / Pena, A. / Frankel, G. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Structure / Year: 2020
Title: Cryoelectron-Microscopic Structure of the pKpQIL Conjugative Pili from Carbapenem-Resistant Klebsiella pneumoniae.
Authors: Weili Zheng / Alejandro Pena / Wen Wen Low / Joshua L C Wong / Gad Frankel / Edward H Egelman /
Abstract: Conjugative pili are important in mediating bacterial conjugation and horizontal gene transfer. Since plasmid transfer can include antibiotic-resistance genes, conjugation is an important mechanism ...Conjugative pili are important in mediating bacterial conjugation and horizontal gene transfer. Since plasmid transfer can include antibiotic-resistance genes, conjugation is an important mechanism in the spread of antibiotic resistance. Filamentous bacteriophages have been shown to exist in two different structural classes: those with a 5-fold rotational symmetry and those with a one-start helix with approximately 5 subunits per turn. Structures for the F and the F-like pED208 conjugation pilus have shown that they have 5-fold rotational symmetry. Here, we report the cryoelectron-microscopic structure of conjugative pili from carbapenem-resistant Klebsiella pneumoniae, encoded on the IncFIIK pKpQIL plasmid, at 3.9 Å resolution and show that it has a one-start helix. These results establish that conjugation pili can exist in at least two structural classes, consistent with other results showing that relatively small perturbations are needed to change the helical symmetry of polymers.
History
DepositionAug 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)329,95382
Polymers300,31141
Non-polymers29,64241
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area173680 Å2
ΔGint-1673 kcal/mol
Surface area83490 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 41 / Rise per n subunits: 2.7 Å / Rotation per n subunits: 77.6 °)

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Components

#1: Protein ...
Pilin / / Conjugal transfer pilin subunit TraA


Mass: 7324.663 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Source: (natural) Klebsiella pneumoniae (bacteria) / References: UniProt: A0A2U0MUX0, UniProt: A6TIG0*PLUS
#2: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
Has ligand of interestN

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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: pKpQIL pili / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
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
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
2Latitudeimage acquisition
4RELION3CTF correction
7RosettaEMmodel fitting
9RELIONinitial Euler assignment
12RELION3D reconstruction
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 77.6 ° / Axial rise/subunit: 2.7 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 263265
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163128 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00822427
ELECTRON MICROSCOPYf_angle_d0.75829725
ELECTRON MICROSCOPYf_dihedral_angle_d18.80613202
ELECTRON MICROSCOPYf_chiral_restr0.043403
ELECTRON MICROSCOPYf_plane_restr0.0063239

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