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

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 1470
TitleMolecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability
KeywordsGTPase / molecular switch / filament / ParM
SampleParM filament
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataA volume file of ParM filament
Methodhelical reconstruction, at 23 Å resolution
AuthorsPopp D / Narita A / Oda T / Fujisawa T / Matsuo H / Nitanai Y / Iwasa M / Maeda K / Onishi H / Maeda Y
CitationEMBO J., 2008, 27, 570-579

EMBO J., 2008, 27, 570-579 StrPapers
Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability.
David Popp / Akihiro Narita / Toshiro Oda / Tetsuro Fujisawa / Hiroshi Matsuo / Yasushi Nitanai / Mitsusada Iwasa / Kayo Maeda / Hirofumi Onishi / Yuichiro Maéda

Validation ReportPDB-ID: 2zhc

SummaryFull reportAbout validation report
DateDeposition: Feb 14, 2008 / Header (metadata) release: Feb 19, 2008 / Map release: Mar 31, 2009 / Last update: Oct 24, 2012

Structure visualization

  • 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
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_1470.map.gz (map file in CCP4 format, 264 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
42 pix
4.01 Å/pix.
= 168.462 Å
40 pix
4.01 Å/pix.
= 160.44 Å
40 pix
4.01 Å/pix.
= 160.44 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.011 Å
Contour Level:0.00012, 9.07E-5 (movie #1):
Minimum - Maximum-6.98964e-05 - 0.000182333
Average (Standard dev.)6.82298e-06 (4.5134e-05)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 160.44 Å / B: 160.44 Å / C: 168.462 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ-55-55-55
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0000.0000.000

Supplemental data

Sample components

Entire ParM filament

EntireName: ParM filament / Number of components: 1 / Oligomeric State: Filament
MassTheoretical: 35 kDa

Component #1: protein, ParM

ProteinName: ParM / a.k.a: ParM / Oligomeric Details: Helical filament / Recombinant expression: Yes / Number of Copies: 10
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

Experimental details

Sample preparation

Specimen statefilament
Helical parametersHand: LEFT HANDED
Sample solutionSpecimen conc.: 0.14 mg/ml
Buffer solution: 10 mM Hepes, 25 mM KCl, 1 mM MgCl2, 1 mM DTT, 5 mM GMPPNP
pH: 7.5
Staining1.0 % uranyl acetate
VitrificationInstrument: NONE / Cryogen name: NONE

Electron microscopy imaging

ImagingMicroscope: JEOL 2010HC
Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER

Image acquisition

Image acquisitionNumber of digital images: 7 / Sampling size: 7 microns

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: EOS / CTF correction: Each filament / Resolution: 23 Å / Resolution method: FSC 0.5

Atomic model buiding

Modeling #1Software: situs / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: Rigid body. After rigid body fitting the structure was refined by energy minimization with program NAMD
Input PDB model: 1MWM
Chain ID: 1MWM_A
Output model

About Yorodumi


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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more