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- PDB-7lhg: Cryo-EM structure of E. coli P pilus tip assembly intermediate Pa... -

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Basic information

Entry
Database: PDB / ID: 7lhg
TitleCryo-EM structure of E. coli P pilus tip assembly intermediate PapC-PapD-PapK-PapG in the first conformation
Components
  • Chaperone protein PapD
  • Fimbrial adapter PapK
  • P fimbria tip G-adhesin PapG-II
  • P fimbrial usher protein PapC
KeywordsCHAPERONE / Cryo-EM / Uropathogenic Escherichia coli / chaperone-usher / P pilus
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / : / cell wall organization / outer membrane-bounded periplasmic space / carbohydrate binding / cell adhesion / extracellular region
Similarity search - Function
Outer membrane usher protein FimD, plug domain / PapC, N-terminal domain / PapG, chaperone-binding / PapG chaperone-binding domain / PapG, carbohydrate-binding domain / PapG, carbohydrate-binding domain superfamily / PapG carbohydrate binding domain / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial ...Outer membrane usher protein FimD, plug domain / PapC, N-terminal domain / PapG, chaperone-binding / PapG chaperone-binding domain / PapG, carbohydrate-binding domain / PapG, carbohydrate-binding domain superfamily / PapG carbohydrate binding domain / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Ubiquitin-like (UB roll) / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / P fimbria tip G-adhesin PapG-II / Chaperone protein PapD / Fimbrial adapter PapK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDu, M. / Yuan, Z. / Werneburg, G. / Henderson, N. / Chauhan, H. / Kovach, A. / Zhao, G. / Johl, J. / Li, H. / Thanassi, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110387 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
CitationJournal: Nat Commun / Year: 2021
Title: Processive dynamics of the usher assembly platform during uropathogenic Escherichia coli P pilus biogenesis.
Authors: Minge Du / Zuanning Yuan / Glenn T Werneburg / Nadine S Henderson / Hemil Chauhan / Amanda Kovach / Gongpu Zhao / Jessica Johl / Huilin Li / David G Thanassi /
Abstract: Uropathogenic Escherichia coli assemble surface structures termed pili or fimbriae to initiate infection of the urinary tract. P pili facilitate bacterial colonization of the kidney and ...Uropathogenic Escherichia coli assemble surface structures termed pili or fimbriae to initiate infection of the urinary tract. P pili facilitate bacterial colonization of the kidney and pyelonephritis. P pili are assembled through the conserved chaperone-usher pathway. Much of the structural and functional understanding of the chaperone-usher pathway has been gained through investigations of type 1 pili, which promote binding to the bladder and cystitis. In contrast, the structural basis for P pilus biogenesis at the usher has remained elusive. This is in part due to the flexible and variable-length P pilus tip fiber, creating structural heterogeneity, and difficulties isolating stable P pilus assembly intermediates. Here, we circumvent these hindrances and determine cryo-electron microscopy structures of the activated PapC usher in the process of secreting two- and three-subunit P pilus assembly intermediates, revealing processive steps in P pilus biogenesis and capturing new conformational dynamics of the usher assembly machine.
History
DepositionJan 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
C: P fimbrial usher protein PapC
D: Chaperone protein PapD
K: Fimbrial adapter PapK
G: P fimbria tip G-adhesin PapG-II


Theoretical massNumber of molelcules
Total (without water)172,0964
Polymers172,0964
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17210 Å2
ΔGint-52 kcal/mol
Surface area66620 Å2

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Components

#1: Protein P fimbrial usher protein PapC


Mass: 88746.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papC, GE554_23855, HJR83_004260 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A773A954
#2: Protein Chaperone protein PapD


Mass: 26833.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papD / Production host: Escherichia coli (E. coli) / References: UniProt: P15319
#3: Protein Fimbrial adapter PapK


Mass: 18895.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papK / Production host: Escherichia coli (E. coli) / References: UniProt: P62532
#4: Protein P fimbria tip G-adhesin PapG-II


Mass: 37620.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papG-II, HJS42_005082 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A798R8B8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PapCDKG / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227396 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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