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- EMDB-21152: Tetradecameric PilQ bound by TsaP heptamer from Pseudomonas aeruginosa -

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Basic information

Entry
Database: EMDB / ID: EMD-21152
TitleTetradecameric PilQ bound by TsaP heptamer from Pseudomonas aeruginosa
Map datasharpened map
Sample
  • Complex: PilQ with TsaP
    • Protein or peptide: Fimbrial assembly protein PilQ
    • Protein or peptide: LysM domain-containing protein
KeywordsType IV pilus / T4P / PilQ / TsaP / secretin / pilotin / type IVa pilus / T4aP / pilus / outer membrane / periplasm / bacterial secretion system / PROTEIN TRANSPORT
Function / homology
Function and homology information


type IV pilus assembly / protein secretion / cell outer membrane
Similarity search - Function
: / Type IV pilus secretin PilQ / : / AMIN domain / AMIN domain / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. ...: / Type IV pilus secretin PilQ / : / AMIN domain / AMIN domain / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein / LysM domain superfamily / Lysin motif / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
Fimbrial assembly protein PilQ / LysM domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMcCallum M / Tammam S
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Structure / Year: 2021
Title: CryoEM map of Pseudomonas aeruginosa PilQ enables structural characterization of TsaP.
Authors: Matthew McCallum / Stephanie Tammam / John L Rubinstein / Lori L Burrows / P Lynne Howell /
Abstract: The type IV pilus machinery is a multi-protein complex that polymerizes and depolymerizes a pilus fiber used for attachment, twitching motility, phage adsorption, natural competence, protein ...The type IV pilus machinery is a multi-protein complex that polymerizes and depolymerizes a pilus fiber used for attachment, twitching motility, phage adsorption, natural competence, protein secretion, and surface-sensing. An outer membrane secretin pore is required for passage of the pilus fiber out of the cell. Herein, the structure of the tetradecameric secretin, PilQ, from the Pseudomonas aeruginosa type IVa pilus system was determined to 4.3 Å and 4.4 Å resolution in the presence and absence of C symmetric spikes, respectively. The heptameric spikes were found to be two tandem C-terminal domains of TsaP. TsaP forms a belt around PilQ and while it is not essential for twitching motility, overexpression of TsaP triggers a signal cascade upstream of PilY1 leading to cyclic di-GMP up-regulation. These results resolve the identity of the spikes identified with Proteobacterial PilQ homologs and may reveal a new component of the surface-sensing cyclic di-GMP signal cascade.
History
DepositionDec 28, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseDec 23, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.46
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.46
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ve2
  • Surface level: 0.46
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21152.png

Downloads & links

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Map

FileDownload / File: emd_21152.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 256 pix.
= 371.2 Å		1.45 Å/pix.
x 256 pix.
= 371.2 Å		1.45 Å/pix.
x 256 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46 / Movie #1: 0.46
Minimum - Maximum-0.27017173 - 1.1162575
Average (Standard dev.)0.0054909023 (±0.07207069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 371.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z371.200371.200371.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2701.1160.005

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Supplemental data

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Additional map: Unsharpened map

Fileemd_21152_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_21152_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_21152_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PilQ with TsaP

EntireName: PilQ with TsaP
Components
  • Complex: PilQ with TsaP
    • Protein or peptide: Fimbrial assembly protein PilQ
    • Protein or peptide: LysM domain-containing protein

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Supramolecule #1: PilQ with TsaP

SupramoleculeName: PilQ with TsaP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Affinity purified PilQ with pulled-down TsaP
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1

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Macromolecule #1: Fimbrial assembly protein PilQ

MacromoleculeName: Fimbrial assembly protein PilQ / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 79.731141 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MNSGLSRLGI ALLAAMFAPA LLAADLEKLD VAALPGDRVE LKLQFDEPVA APRGYTIEQP ARIALDLPGV QNKLGTKNRE LSVGNTRSV TVVEAKDRTR LIINLTALSS YTTRVEGNNL FVVVGNSPHH HHHHHHAGAS VASAAPVKAS PAPASYAQPI K PKPYVPAG ...String:
MNSGLSRLGI ALLAAMFAPA LLAADLEKLD VAALPGDRVE LKLQFDEPVA APRGYTIEQP ARIALDLPGV QNKLGTKNRE LSVGNTRSV TVVEAKDRTR LIINLTALSS YTTRVEGNNL FVVVGNSPHH HHHHHHAGAS VASAAPVKAS PAPASYAQPI K PKPYVPAG RAIRNIDFQR GEKGEGNVVI DLSDPTLSPD IQEQGGKIRL DFAKTQLPDA LRVRLDVKDF ATPVQFVNAS AQ SDRTSIT IEPSGLYDYL VYQTDNRLTV SIKPMTTEDA ERRKKDNFAY TGEKLSLNFQ DIDVRSVLQL IADFTDLNLV ASD TVQGNI TLRLQNVPWD QALDLVLKTK GLDKRKLGNV LLVAPADEIA ARERQELEAQ KQIAELAPLR RELIQVNYAK AADI AKLFQ SVTSDGGQEG KEGGRGSITV DDRTNSIIAY QPQERLDELR RIVSQLDIPV RQVMIEARIV EANVGYDKSL GVRWG GAYH KGNWSGYGKD GNIGIKDEDG MNCGPIAGSC TFPTTGTSKS PSPFVDLGAK DATSGIGIGF ITDNIILDLQ LSAMEK TGN GEIVSQPKVV TSDKETAKIL KGSEVPYQEA SSSGATSTSF KEAALSLEVT PQITPDNRII VEVKVTKDAP DYQNMLN GV PPINKNEVNA KILVNDGETI VIGGVFSNEQ SKSVEKVPFL GELPYLGRLF RRDTVTDRKN ELLVFLTPRI MNNQAIAI G RGHHHHHHHH

UniProtKB: Fimbrial assembly protein PilQ

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Macromolecule #2: LysM domain-containing protein

MacromoleculeName: LysM domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 37.632902 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MRKSLVALLL LAASGLAQAQ VDLREGHPDR YTVVRGDTLW DISGKFLRQP WKWPELWHAN PQIQNPHLIY PGDTLSLVYV DGQPRLVLN RGESRGTIKL SPKIRSTPIA EAIPTIPLDK INSFLLANRI VDDEKTFTSA PYIVAGNAER IVSGTGDRIY A RGKFADGQ ...String:
MRKSLVALLL LAASGLAQAQ VDLREGHPDR YTVVRGDTLW DISGKFLRQP WKWPELWHAN PQIQNPHLIY PGDTLSLVYV DGQPRLVLN RGESRGTIKL SPKIRSTPIA EAIPTIPLDK INSFLLANRI VDDEKTFTSA PYIVAGNAER IVSGTGDRIY A RGKFADGQ PAYGIFRQGK VYIDPKTKEV LGINADDIGG GEVVATEGDV ATLALTRTTQ EVRLGDRLFP TEERAVNSTF MP GEPSREV KGEIIDVPRG VTQIGQFDVV TLNRGQRDGL AEGNVLAIYK VGETVRDRVT GESVKIPDER AGLLMVFRTY KKL SYALVL MASRPLSVTD RVQNP

UniProtKB: LysM domain-containing protein

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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: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.7 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Starting models generated in Phyre2 and I-TASSER
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 47468
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 98
Output model

PDB-6ve2:
Tetradecameric PilQ bound by TsaP heptamer from Pseudomonas aeruginosa

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