[English] 日本語
Yorodumi
- EMDB-1470: Molecular structure of the ParM polymer and the mechanism leading... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1470
TitleMolecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability
Map dataA volume file of ParM filament
Sample
  • Sample: ParM filament
  • Protein or peptide: ParM
KeywordsGTPase / molecular switch / filament / ParM
Function / homologyPlasmid segregation protein ParM/StbA / : / : / Plasmid segregation protein ParM, N-terminal / Plasmid segregation protein ParM, C-terminal / plasmid partitioning / ATPase, nucleotide binding domain / identical protein binding / Plasmid segregation protein ParM
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / negative staining / Resolution: 23.0 Å
AuthorsPopp D / Narita A / Oda T / Fujisawa T / Matsuo H / Nitanai Y / Iwasa M / Maeda K / Onishi H / Maeda Y
CitationJournal: EMBO J / Year: 2008
Title: Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability.
Authors: David Popp / Akihiro Narita / Toshiro Oda / Tetsuro Fujisawa / Hiroshi Matsuo / Yasushi Nitanai / Mitsusada Iwasa / Kayo Maeda / Hirofumi Onishi / Yuichiro Maéda /
Abstract: ParM is a prokaryotic actin homologue, which ensures even plasmid segregation before bacterial cell division. In vivo, ParM forms a labile filament bundle that is reminiscent of the more complex ...ParM is a prokaryotic actin homologue, which ensures even plasmid segregation before bacterial cell division. In vivo, ParM forms a labile filament bundle that is reminiscent of the more complex spindle formed by microtubules partitioning chromosomes in eukaryotic cells. However, little is known about the underlying structural mechanism of DNA segregation by ParM filaments and the accompanying dynamic instability. Our biochemical, TIRF microscopy and high-pressure SAX observations indicate that polymerization and disintegration of ParM filaments is driven by GTP rather than ATP and that ParM acts as a GTP-driven molecular switch similar to a G protein. Image analysis of electron micrographs reveals that the ParM filament is a left-handed helix, opposed to the right-handed actin polymer. Nevertheless, the intersubunit contacts are similar to those of actin. Our atomic model of the ParM-GMPPNP filament, which also fits well to X-ray fibre diffraction patterns from oriented gels, can explain why after nucleotide release, large conformational changes of the protomer lead to a breakage of intra- and interstrand interactions, and thus to the observed disintegration of the ParM filament after DNA segregation.
History
DepositionFeb 14, 2008-
Header (metadata) releaseFeb 19, 2008-
Map releaseMar 31, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9.0672E-5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 9.0672E-5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1470.gif

Downloads & links

-
Map

FileDownload / File: emd_1470.map.gz / Format: CCP4 / Size: 257.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA volume file of ParM filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.01 Å/pix.
x 42 pix.
= 168.462 Å		4.01 Å/pix.
x 40 pix.
= 160.44 Å		4.01 Å/pix.
x 40 pix.
= 160.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.011 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00012 / Movie #1: 9.07E-5
Minimum - Maximum-0.0000698964 - 0.000182333
Average (Standard dev.)0.00000682298 (±0.000045134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions404042
Spacing404042
CellA: 160.44 Å / B: 160.44 Å / C: 168.462 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.0114.0114.011
M x/y/z404042
origin x/y/z0.0000.0000.000
length x/y/z160.440160.440168.462
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS404042
D min/max/mean-0.0000.0000.000

-
Supplemental data

-
Sample components

-
Entire : ParM filament

EntireName: ParM filament
Components
  • Sample: ParM filament
  • Protein or peptide: ParM

-
Supramolecule #1000: ParM filament

SupramoleculeName: ParM filament / type: sample / ID: 1000 / Oligomeric state: Filament / Number unique components: 1
Molecular weightTheoretical: 35 KDa

-
Macromolecule #1: ParM

MacromoleculeName: ParM / type: protein_or_peptide / ID: 1 / Name.synonym: ParM / Number of copies: 10 / Oligomeric state: Helical filament / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.14 mg/mL
BufferpH: 7.5
Details: 10 mM Hepes, 25 mM KCl, 1 mM MgCl2, 1 mM DTT, 5 mM GMPPNP
StainingType: NEGATIVE / Details: 1.0 % uranyl acetate
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 2010HC
Image recordingDigitization - Sampling interval: 7 µm / Number real images: 7
Electron beamAcceleration voltage: 100 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: OTHER

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EOS
CTF correctionDetails: Each filament

-
Atomic model buiding 1

Initial modelPDB ID:

1mwm


Chain - Chain ID: A
SoftwareName: situs
DetailsPDBEntryID_givenInChain. Protocol: Rigid body. After rigid body fitting the structure was refined by energy minimization with program NAMD
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2zhc:
ParM filament

+
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