[English] 日本語
Yorodumi
- EMDB-51732: Tad pilus alignment complex protein RcpC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51732
TitleTad pilus alignment complex protein RcpC
Map data
Sample
  • Complex: Dodecameric assembly of RcpC
    • Protein or peptide: RcpC
KeywordsTad pilus / Pseudomonas aeruginosa / membrane protein / biofilms
Function / homologyPilus assembly, Flp-type CpaB / Flp pilus assembly protein RcpC/CpaB domain / Flp pilus assembly protein RcpC/CpaB / SAF domain / SAF / SAF domain / RcpC
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsEvans SL / Peretiazhko I / Bergeron JRC
Funding support France, United Kingdom, 2 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGY0080/2021 France
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R009759/2 United Kingdom
CitationJournal: To Be Published
Title: The structure of the Tad pilus alignment complex reveals a periplasmic conduit for pilus extension
Authors: Evans SL / Peretiazhko I / Bergeron JRC
History
DepositionOct 4, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51732.png

Downloads & links

-
Map

FileDownload / File: emd_51732.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0574
Minimum - Maximum-0.0019689705 - 1.7239542
Average (Standard dev.)0.00241366 (±0.035540517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_51732_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51732_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dodecameric assembly of RcpC

EntireName: Dodecameric assembly of RcpC
Components
  • Complex: Dodecameric assembly of RcpC
    • Protein or peptide: RcpC

-
Supramolecule #1: Dodecameric assembly of RcpC

SupramoleculeName: Dodecameric assembly of RcpC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 412 KDa

-
Macromolecule #1: RcpC

MacromoleculeName: RcpC / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 29.816893 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNAHAPSVAP ASATVDASLE KLERKPVLVA SRDLPALAVI GRDDLSVELL RTAPVGSYDR PEALLGKRVW VAVPAGSILS AATLEPGGP LARTIRPDER AMAIAVDEVV GGGGFVLPGD YVDVMLFVRD ERDGESTPLA QLVLPGVRVL TYGERIAVGS D GQDRSNQE ...String:
MNAHAPSVAP ASATVDASLE KLERKPVLVA SRDLPALAVI GRDDLSVELL RTAPVGSYDR PEALLGKRVW VAVPAGSILS AATLEPGGP LARTIRPDER AMAIAVDEVV GGGGFVLPGD YVDVMLFVRD ERDGESTPLA QLVLPGVRVL TYGERIAVGS D GQDRSNQE KDPRPPRTAV LAVPEDGVAR LMLASQAGSL RLAIRSKDEE LYRREQEGAL LQASLGAPSA ALSLDQLLER RK PTAPSVR SAAPRVPVAN GVTVYRGSAM THEAPLEHHH HHH

UniProtKB: RcpC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 14847 / Average electron dose: 45.0 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: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 14150712
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1108916
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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