[English] 日本語
Yorodumi
- PDB-3crf: Electron Microscopy model of the Saf Pilus- Type B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3crf
TitleElectron Microscopy model of the Saf Pilus- Type B
Components(Outer membrane proteinVirulence-related outer membrane protein family) x 3
KeywordsMEMBRANE PROTEIN / SafA protein polymer / Type B Saf Pilus / Fibril Protein
Function / homologySaf-pilin pilus formation protein / Saf-pilin pilus formation protein / Dr-adhesin superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Outer membrane protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / negative staining / Resolution: 17 Å
AuthorsSalih, O. / Remaut, H. / Waksman, G. / Orlova, E.V.
CitationJournal: J Mol Biol / Year: 2008
Title: Structural analysis of the Saf pilus by electron microscopy and image processing.
Authors: Osman Salih / Han Remaut / Gabriel Waksman / Elena V Orlova /
Abstract: Bacterial pili are important virulence factors involved in host cell attachment and/or biofilm formation, key steps in establishing and maintaining successful infection. Here we studied Salmonella ...Bacterial pili are important virulence factors involved in host cell attachment and/or biofilm formation, key steps in establishing and maintaining successful infection. Here we studied Salmonella atypical fimbriae (or Saf pili), formed by the conserved chaperone/usher pathway. In contrast to the well-established quaternary structure of typical/FGS-chaperone assembled, rod-shaped, chaperone/usher pili, little is known about the supramolecular organisation in atypical/FGL-chaperone assembled fimbriae. In our study, we have used negative stain electron microscopy and single-particle image analysis to determine the three-dimensional structure of the Salmonella typhimurium Saf pilus. Our results show atypical/FGL-chaperone assembled fimbriae are composed of highly flexible linear multi-subunit fibres that are formed by globular subunits connected to each other by short links giving a "beads on a string"-like appearance. Quantitative fitting of the atomic structure of the SafA pilus subunit into the electron density maps, in combination with linker modelling and energy minimisation, has enabled analysis of subunit arrangement and intersubunit interactions in the Saf pilus. Short intersubunit linker regions provide the molecular basis for flexibility of the Saf pilus by acting as molecular hinges allowing a large range of movement between consecutive subunits in the fibre.
History
DepositionApr 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1495
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane protein
B: Outer membrane protein
C: Outer membrane protein


Theoretical massNumber of molelcules
Total (without water)30,3333
Polymers30,3333
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Outer membrane protein / Virulence-related outer membrane protein family / SAFA PILUS SUBUNIT


Mass: 12992.533 Da / Num. of mol.: 1
Fragment: core pilin domain, N-terminal deleted, UNP residues 48-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: safA / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q8ZRK4
#2: Protein Outer membrane protein / Virulence-related outer membrane protein family / SAFA PILUS SUBUNIT


Mass: 15270.004 Da / Num. of mol.: 1 / Fragment: core pilin domain, UNP residues 27-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: safA / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q8ZRK4
#3: Protein/peptide Outer membrane protein / Virulence-related outer membrane protein family / SAFA N-TERMINAL EXTENSION


Mass: 2070.237 Da / Num. of mol.: 1 / Fragment: N-TERMINAL EXTENSION, UNP residues 27-45 / Source method: obtained synthetically / Details: SafANte-N-terminal extension / References: UniProt: Q8ZRK4

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: Wild-type SafA pili / Type: COMPLEX
Details: Stained with 2% ammonium molybdate. Type B Saf pilus. Fibre.
Buffer solutionName: 10 mM TRIS-HCl (pH 8) and 10 mM NaCl / pH: 8 / Details: 10 mM TRIS-HCl (pH 8) and 10 mM NaCl
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Ammonium Molybdate
Specimen supportDetails: Continuous-carbon film

-
Electron microscopy imaging

MicroscopyModel: FEI TECNAI 10 / Date: Apr 23, 2004
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 44000 X / Nominal defocus max: 900 nm / Nominal defocus min: 400 nm / Cs: 2.4 mm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM

-
Processing

EM software
IDNameCategory
1UROmodel fitting
2IMAGIC3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Cross-common lines / Resolution: 17 Å / Num. of particles: 8500 / Actual pixel size: 1.591 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: Correlation coefficient / Details: REFINEMENT PROTOCOL--Rigid body
Atomic model buildingPDB-ID: 2CO4

2co4


Accession code: 2CO4 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 0 0 2135

+
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