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- EMDB-23339: Cryo-EM map of E. coli P pilus tip assembly intermediate PapC-Pap... -

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Basic information

Entry
Database: EMDB / ID: EMD-23339
TitleCryo-EM map of E. coli P pilus tip assembly intermediate PapC-PapD-PapK-PapG in the first 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
KeywordsCryo-EM / Uropathogenic Escherichia coli / chaperone-usher / P pilus / CHAPERONE
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / 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: 3.8 Å
AuthorsDu M / Yuan Z
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-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lhg
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23339.png

Downloads & links

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Map

FileDownload / File: emd_23339.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 200 pix.
= 205.8 Å		1.03 Å/pix.
x 200 pix.
= 205.8 Å		1.03 Å/pix.
x 200 pix.
= 205.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.029 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.057524417 - 0.10000229
Average (Standard dev.)0.00079634425 (±0.004072091)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
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/NS000
NC/NR/NS200200200
D min/max/mean-0.0580.1000.001

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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)

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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

UniProtKB: UNIPROTKB: A0A773A954

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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: 26.833746 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIRKKILMAA IPLFVISGAD AAVSLDRTRA VFDGSEKSMT LDISNDNKQL PYLAQAWIEN ENQEKIITGP VIATPPVQRL EPGAKSMVR LSTTPDISKL PQDRESLFYF NLREIPPRSE KANVLQIALQ TKIKLFYRPA AIKTRPNEVW QDQLILNKVS G GYRIENPT ...String:
MIRKKILMAA IPLFVISGAD AAVSLDRTRA VFDGSEKSMT LDISNDNKQL PYLAQAWIEN ENQEKIITGP VIATPPVQRL EPGAKSMVR LSTTPDISKL PQDRESLFYF NLREIPPRSE KANVLQIALQ TKIKLFYRPA AIKTRPNEVW QDQLILNKVS G GYRIENPT PYYVTVIGLG GSEKQAEEGE FETVMLSPRS EQTVKSANYN TPYLSYINDY GGRPVLSFIC NGSRCSVKKE K

UniProtKB: Chaperone protein PapD

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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

UniProtKB: Fimbrial adapter PapK

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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

UniProtKB: P fimbria tip G-adhesin PapG-II

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

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 227396
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

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

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