[English] 日本語
Yorodumi
- EMDB-16810: RcpA-TadD with C13 symmetry from the Pseudomonas aeruginosa Tight... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16810
TitleRcpA-TadD with C13 symmetry from the Pseudomonas aeruginosa Tight Adherence Secretion System
Map dataRcpA-TadD with C13 symmetry from the Pseudomonas aeruginosa Tigh Adherence Secretion System
Sample
  • Complex: RcpA-TadD with C13 symmetry
    • Protein or peptide: RcpA
    • Protein or peptide: TPR repeat-containing protein PA4299
KeywordsSecretin / Pilotin / RcpA / TadD / TAD / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
RcpA / TPR repeat-containing protein PA4299
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16810.png

Downloads & links

-
Map

FileDownload / File: emd_16810.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRcpA-TadD with C13 symmetry from the Pseudomonas aeruginosa Tigh Adherence Secretion System
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. 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-0.06529311 - 0.15497226
Average (Standard dev.)0.00018274676 (±0.0022917364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: RcpA-TadD with C13 symmetry from the Pseudomonas aeruginosa...

Fileemd_16810_half_map_1.map
AnnotationRcpA-TadD with C13 symmetry from the Pseudomonas aeruginosa Tigh Adherence Secretion System
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RcpA-TadD with C13 symmetry from the Pseudomonas aeruginosa...

Fileemd_16810_half_map_2.map
AnnotationRcpA-TadD with C13 symmetry from the Pseudomonas aeruginosa Tigh Adherence Secretion System
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RcpA-TadD with C13 symmetry

EntireName: RcpA-TadD with C13 symmetry
Components
  • Complex: RcpA-TadD with C13 symmetry
    • Protein or peptide: RcpA
    • Protein or peptide: TPR repeat-containing protein PA4299

-
Supramolecule #1: RcpA-TadD with C13 symmetry

SupramoleculeName: RcpA-TadD with C13 symmetry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 900 KDa

-
Macromolecule #1: RcpA

MacromoleculeName: RcpA / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 45.507402 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHRSTGIGVS RWLGGLLGVA LALPALALPQ GCIELLAQAP RVDVVQGQQR DLRLAVPIER LAIGDPKIAD VQLLDRRGFL VTGKEQGST SLLIWTGCSP EPLRSLVEVE GRGSVDTRGA PAFTVGAAEE LPNQVQTDIR FVEVSRSKLK QASTSFVRRG G NLWVLGAP ...String:
MHRSTGIGVS RWLGGLLGVA LALPALALPQ GCIELLAQAP RVDVVQGQQR DLRLAVPIER LAIGDPKIAD VQLLDRRGFL VTGKEQGST SLLIWTGCSP EPLRSLVEVE GRGSVDTRGA PAFTVGAAEE LPNQVQTDIR FVEVSRSKLK QASTSFVRRG G NLWVLGAP GSLGDIKVNA DGSGLGGTFG TGSSGFNLIF GGGKWLSFMN ALEGSGFAYT LARPSLVAMS GQSASFLAGG EF PIPVPNG TNDNVTIEYK EFGIRLTLTP TVMNNRRIAL KVAPEVSELD YSAGIQSGGV AVPALRVRRT DTSVMLADGE SFV ISGLTS SNSVSNVDKF PWLGDIPILG AFFRSTKLDK DDRELLMIVT PHLVQPLAAD AQLPDLPGEG LRHYDPGFSR LYFL ERGEY DGQQNDTGLS DSAWSHPQFE K

UniProtKB: RcpA

-
Macromolecule #2: TPR repeat-containing protein PA4299

MacromoleculeName: TPR repeat-containing protein PA4299 / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 27.759648 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKALIGIGLC AALLGGCAAL PGRDGPRECS QQLGQEQELQ MNMVRDMIRE GRLHAALANL ESMPPGLLDV REERALILRR IGDPRARAE YQALLETCKA PEAHHGLGLL ALRNGDSARA VLELREAARL RPTESRFRND LGVALLKRGD RVGARFEFIT A LELQQGGK ...String:
MKALIGIGLC AALLGGCAAL PGRDGPRECS QQLGQEQELQ MNMVRDMIRE GRLHAALANL ESMPPGLLDV REERALILRR IGDPRARAE YQALLETCKA PEAHHGLGLL ALRNGDSARA VLELREAARL RPTESRFRND LGVALLKRGD RVGARFEFIT A LELQQGGK LPATNLLGLL YLQGDREDAQ RLIERLQLDA RDIRAAEARA RSWGAVPTPG AAPASDDPLA ELPAEANMHT AM ANEAPGS DYKDDDDK

UniProtKB: TPR repeat-containing protein PA4299

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4Shepes
100.0 mMNaClsodium chloride
1.0 mMC10H16N2O8EDTA
0.06 %C24H46O11bDDM

Details: 50 mM Hepes pH 8, 100 mM NaCl, 1 mM EDTA, 0.06% bDDM
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: The grid was coated with graphene oxide prior to use
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
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 opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119534
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more