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- EMDB-16818: RcpA-TadD local refinement map -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-16818
TitleRcpA-TadD local refinement map
Map dataRcpA-TadD Local refinement map
Sample
  • Complex: RcpA-TadD from the Paseudomonas aeruginosa Tad secretion system
    • Protein or peptide: RcpA
    • Protein or peptide: TadD
KeywordsRcpA / TadD / Secretin / Pilotin / Tight adherence secretion system / local refinement / MEMBRANE PROTEIN
Function / homology
Function and homology information


type II protein secretion system complex / protein secretion / plasma membrane
Similarity search - Function
Uncharacterised conserved protein UCP029658, TPR / Pilus formation protein, N-terminal / Pilus formation protein N terminal region / GspD/PilQ family / : / Type II/III secretion system / Bacterial type II and III secretion system protein / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat ...Uncharacterised conserved protein UCP029658, TPR / Pilus formation protein, N-terminal / Pilus formation protein N terminal region / GspD/PilQ family / : / Type II/III secretion system / Bacterial type II and III secretion system protein / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
RcpA / TPR repeat-containing protein PA4299
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsTassinari M / Low HH
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust215553/Z/19/Z United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Assembly mechanism of a Tad secretion system secretin-pilotin complex.
Authors: Matteo Tassinari / Marta Rudzite / Alain Filloux / Harry H Low /
Abstract: The bacterial Tight adherence Secretion System (TadSS) assembles surface pili that drive cell adherence, biofilm formation and bacterial predation. The structure and mechanism of the TadSS is mostly ...The bacterial Tight adherence Secretion System (TadSS) assembles surface pili that drive cell adherence, biofilm formation and bacterial predation. The structure and mechanism of the TadSS is mostly unknown. This includes characterisation of the outer membrane secretin through which the pilus is channelled and recruitment of its pilotin. Here we investigate RcpA and TadD lipoprotein from Pseudomonas aeruginosa. Light microscopy reveals RcpA colocalising with TadD in P. aeruginosa and when heterologously expressed in Escherichia coli. We use cryogenic electron microscopy to determine how RcpA and TadD assemble a secretin channel with C13 and C14 symmetries. Despite low sequence homology, we show that TadD shares a similar fold to the type 4 pilus system pilotin PilF. We establish that the C-terminal four residues of RcpA bind TadD - an interaction essential for secretin formation. The binding mechanism between RcpA and TadD appears distinct from known secretin-pilotin pairings in other secretion systems.
History
DepositionMar 9, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16818.png

Downloads & links

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Map

FileDownload / File: emd_16818.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRcpA-TadD Local refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 250 pix.
= 275. Å		1.1 Å/pix.
x 250 pix.
= 275. Å		1.1 Å/pix.
x 250 pix.
= 275. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.03286825 - 0.07306445
Average (Standard dev.)0.0005981514 (±0.0025951175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 275.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: RcpA-TadD Local refinement map

Fileemd_16818_half_map_1.map
AnnotationRcpA-TadD Local refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: RcpA-TadD Local refinement map

Fileemd_16818_half_map_2.map
AnnotationRcpA-TadD Local refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RcpA-TadD from the Paseudomonas aeruginosa Tad secretion system

EntireName: RcpA-TadD from the Paseudomonas aeruginosa Tad secretion system
Components
  • Complex: RcpA-TadD from the Paseudomonas aeruginosa Tad secretion system
    • Protein or peptide: RcpA
    • Protein or peptide: TadD

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Supramolecule #1: RcpA-TadD from the Paseudomonas aeruginosa Tad secretion system

SupramoleculeName: RcpA-TadD from the Paseudomonas aeruginosa Tad secretion system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 900 KDa

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Macromolecule #1: RcpA

MacromoleculeName: RcpA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHRSTGIGVS RWLGGLLGVA LALPALALPQ GCIELLAQAP RVDVVQGQQR DLRLAVPIER LAIGDPKIAD VQLLDRRGFL VTGKEQGSTS LLIWTGCSPE PLRSLVEVEG RGSVDTRGAP AFTVGAAEEL PNQVQTDIRF VEVSRSKLKQ ASTSFVRRGG NLWVLGAPGS ...String:
MHRSTGIGVS RWLGGLLGVA LALPALALPQ GCIELLAQAP RVDVVQGQQR DLRLAVPIER LAIGDPKIAD VQLLDRRGFL VTGKEQGSTS LLIWTGCSPE PLRSLVEVEG RGSVDTRGAP AFTVGAAEEL PNQVQTDIRF VEVSRSKLKQ ASTSFVRRGG NLWVLGAPGS LGDIKVNADG SGLGGTFGTG SSGFNLIFGG GKWLSFMNAL EGSGFAYTLA RPSLVAMSGQ SASFLAGGEF PIPVPNGTND NVTIEYKEFG IRLTLTPTVM NNRRIALKVA PEVSELDYSA GIQSGGVAVP ALRVRRTDTS VMLADGESFV ISGLTSSNSV SNVDKFPWLG DIPILGAFFR STKLDKDDRE LLMIVTPHLV QPLAADAQLP DLPGEGLRHY DPGFSRLYFL ERGEYDGQQN DTGLSDSAWS HPQFEK

UniProtKB: RcpA

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Macromolecule #2: TadD

MacromoleculeName: TadD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKALIGIGLC AALLGGCAAL PGRDGPRECS QQLGQEQELQ MNMVRDMIRE GRLHAALANL ESMPPGLLDV REERALILRR IGDPRARAEY QALLETCKAP EAHHGLGLLA LRNGDSARAV LELREAARLR PTESRFRNDL GVALLKRGDR VGARFEFITA LELQQGGKLP ...String:
MKALIGIGLC AALLGGCAAL PGRDGPRECS QQLGQEQELQ MNMVRDMIRE GRLHAALANL ESMPPGLLDV REERALILRR IGDPRARAEY QALLETCKAP EAHHGLGLLA LRNGDSARAV LELREAARLR PTESRFRNDL GVALLKRGDR VGARFEFITA LELQQGGKLP ATNLLGLLYL QGDREDAQRL IERLQLDARD IRAAEARARS WGAVPTPDAA PASDDPLAEL PAEANMHTAM ANEAPGSDYK DDDDK

UniProtKB: TPR repeat-containing protein PA4299

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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
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4Shepes
100.0 mMNaClsodium chloride
2.0 mMC10H16N2O8edta
0.06 %C24H46O11bDDM

Details: 50 mM Hepes pH 8, 100 mM NaCl, 2 mM EDTA, 0.06 % bDDM
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 887691
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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