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- EMDB-23340: Cryo-EM map of E. coli P pilus tip assembly intermediate PapC-Pap... -

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Basic information

Entry
Database: EMDB / ID: EMD-23340
TitleCryo-EM map of E. coli P pilus tip assembly intermediate PapC-PapD-PapK-PapG in the second conformation
Map data
Sample
  • Complex: PapCDKG
    • Protein or peptide: P fimbrial usher protein PapC
    • Protein or peptide: Chaperone protein PapD
    • Protein or peptide: Fimbrial adapter PapK
    • Protein or peptide: P fimbria tip G-adhesin PapG-II
Function / homology
Function and homology information


pilus / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space / carbohydrate binding / cell adhesion / extracellular region
Similarity search - Function
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 ...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 / Immunoglobulin-like fold
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 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, 2 items
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, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lhh
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23340.png

Downloads & links

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Map

FileDownload / File: emd_23340.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.029 Å
Density
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.043072507 - 0.089063354
Average (Standard dev.)0.0019583763 (±0.0070372582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin666
Dimensions200200200
Spacing200200200
CellA=B=C: 205.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0291.0291.029
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z205.800205.800205.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS666
NC/NR/NS200200200
D min/max/mean-0.0430.0890.002

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Supplemental data

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Sample components

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Entire : PapCDKG

EntireName: PapCDKG
Components
  • Complex: PapCDKG
    • Protein or peptide: P fimbrial usher protein PapC
    • Protein or peptide: Chaperone protein PapD
    • Protein or peptide: Fimbrial adapter PapK
    • Protein or peptide: P fimbria tip G-adhesin PapG-II

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Supramolecule #1: PapCDKG

SupramoleculeName: PapCDKG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: P fimbrial usher protein PapC

MacromoleculeName: P fimbrial usher protein PapC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 88.746297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VEFNTDVLDA ADKKNIDFTR FSEAGYVLPG QYLLDVIVNG QSISPASLQI SFVEPQSSGD KAEKKLPQAC LTSDMVRLMG LTAESLDKV VYWHDGQCAD FHGLPGVDIR PDTGAGVLRI NMPQARLEYS DATWLPPSRW DDGIPGLMLD YNLNGTVSRN Y QGGDSHQF ...String:
VEFNTDVLDA ADKKNIDFTR FSEAGYVLPG QYLLDVIVNG QSISPASLQI SFVEPQSSGD KAEKKLPQAC LTSDMVRLMG LTAESLDKV VYWHDGQCAD FHGLPGVDIR PDTGAGVLRI NMPQARLEYS DATWLPPSRW DDGIPGLMLD YNLNGTVSRN Y QGGDSHQF SYNGTVGGNL GPWRLRADYQ GSQEQSRYNG EKTTNRNFTW SRFYLFRAIP RWRANLTLGE NNINSDIFRS WS YTGASLE SDDRMLPPRL RGYAPQITGI AETNARVVVS QQGRVLYDSM VPAGPFSIQD LDSSVRGRLD VEVIEQNGRK KTF QVDTAS VPYLTRPGQV RYKLVSGRSR GYGHETEGPV FATGEASWGL SNQWSLYGGA VLAGDYNALA AGAGWDLGVP GTLS ADITQ SVARIEGERT FQGKSWRLSY SKRFDNADAD ITFAGYRFSE RNYMTMEQYL NARYRNDYSS REKEMYTVTL NKNVA DWNT SFNLQYSRQT YWDIRKTDYY TVSVNRYFNV FGLQGVAVGL SASRSKYLGR DNDSAYLRIS VPLGTGTASY SGSMSN DRY VNMAGYTDTF NDGLDSYSLN AGLNSGGGLT SQRQINAYYS HRSPLANLSA NIASLQKGYT SFGVSASGGA TITGKDA AL HAGGMSGGTR LLVDTDGVGG VPVDGGQVVT NRWGTGVVTD ISSYYRNTTS VDLKRLPDDV EATRSVVESA LTEGAIGY R KFSVLKGKRL FAILRLADGS QPPFGASVTS EKGRELGMVA DEGLAWLSGV TPGETLSVNW DGKIQCQVNV PETAISDQQ LLLPCTPQK

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Macromolecule #2: Chaperone protein PapD

MacromoleculeName: Chaperone protein PapD / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.589895 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AVSLDRTRAV FDGSEKSMTL DISNDNKQLP YLAQAWIENE NQEKIITGPV IATPPVQRLE PGAKSMVRLS TTPDISKLPQ DRESLFYFN LREIPPRSEK ANVLQIALQT KIKLFYRPAA IKTRPNEVWQ DQLILNKVSG GYRIENPTPY YVTVIGLGGS E KQAEEGEF ...String:
AVSLDRTRAV FDGSEKSMTL DISNDNKQLP YLAQAWIENE NQEKIITGPV IATPPVQRLE PGAKSMVRLS TTPDISKLPQ DRESLFYFN LREIPPRSEK ANVLQIALQT KIKLFYRPAA IKTRPNEVWQ DQLILNKVSG GYRIENPTPY YVTVIGLGGS E KQAEEGEF ETVMLSPRSE QTVKSANYNT PYLSYINDYG GRPVLSFICN GSRCSVKKEK

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Macromolecule #3: Fimbrial adapter PapK

MacromoleculeName: Fimbrial adapter PapK / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.895492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIKSTGALLL FAALSAGQAI ASDVAFRGNL LDRPCHVSGD SLNKHVVFKT RASRDFWYPP GRSPTESFVI RLENCHATAV GKIVTLTFK GTEEAALPGH LKVTGVNAGR LGIALLDTDG SSLLKPGTSH NKGQGEKVTG NSLELPFGAY VVATPEALRT K SVVPGDYE ATATFELTYR

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Macromolecule #4: P fimbria tip G-adhesin PapG-II

MacromoleculeName: P fimbria tip G-adhesin PapG-II / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 37.62057 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKWFPALLF SLCVSGESSA WNNIVFYSLG DVNSYQGGNV VITQRPQFIT SWRPGIATVT WNQCNGPGFA DGFWAYYREY IAWVVFPKK VMTQNGYPLF IEVHNKGSWS EENTGDNDSY FFLKGYKWDE RAFDAGNLCQ KPGETTRLTE KFDDIIFKVA L PADLPLGD ...String:
MKKWFPALLF SLCVSGESSA WNNIVFYSLG DVNSYQGGNV VITQRPQFIT SWRPGIATVT WNQCNGPGFA DGFWAYYREY IAWVVFPKK VMTQNGYPLF IEVHNKGSWS EENTGDNDSY FFLKGYKWDE RAFDAGNLCQ KPGETTRLTE KFDDIIFKVA L PADLPLGD YSVKIPYTSG MQRHFASYLG ARFKIPYNVA KTLPRENEML FLFKNIGGCR PSAQSLEIKH GDLSINSANN HY AAQTLSV SCDVPANIRF MLLRNTTPTY SHGKKFSVGL GHGWDSIVSV NGVDTGETTM RWYKAGTQNL TIGSRLYGES SKI QPGVLS GSATLLMILP

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131650

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7lhh:
Cryo-EM structure of E. coli P pilus tip assembly intermediate PapC-PapD-PapK-PapG in the second conformation

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