[English] 日本語
- EMDB-5129: Reconstruction of ParM in the open state using cryo-EM -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 5129
TitleReconstruction of ParM in the open state using cryo-EM
Keywordspolymorphic protein polymers
Map dataReconstruction of ParM in the open state
Methodhelical reconstruction
AuthorsGalkin VE / Orlova A / Rivera C / Mullins RD / Egelman EH
CitationStructure, 2009, 17, 1253-1264

Structure, 2009, 17, 1253-1264 Yorodumi Papers
Structural polymorphism of the ParM filament and dynamic instability.
Vitold E Galkin / Albina Orlova / Chris Rivera / R Dyche Mullins / Edward H Egelman

Validation ReportPDB-ID: 3iky

SummaryFull reportAbout validation report
DateDeposition: Aug 6, 2009 / Header (metadata) release: Aug 24, 2009 / Map release: Sep 17, 2009 / Last update: Apr 2, 2014

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2000
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2000
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3iky
  • Surface level: 2000
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links


Fileemd_5129.map.gz (map file in CCP4 format, 7814 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
2.38 Å/pix.
= 476. Å
100 pix
2.38 Å/pix.
= 238. Å
100 pix
2.38 Å/pix.
= 238. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.38 Å
Contour Level:1000 (by author), 2000 (movie #1):
Minimum - Maximum-974.88922119 - 6558.34570313
Average (Standard dev.)112.41428375 (600.58074951)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 238.00002 Å / B: 238.00002 Å / C: 476.00003 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.382.382.38
M x/y/z100100200
origin x/y/z0.0000.0000.000
length x/y/z238.000238.000476.000
start NX/NY/NZ-34-26-72
MAP C/R/S123
start NC/NR/NS-50-50-100
D min/max/mean-974.8896558.346112.414

Supplemental data

Sample components

Entire ParM

EntireName: ParM / Number of components: 1

Component #1: protein, ParM

ProteinName: ParM / a.k.a: ParM / Recombinant expression: No
SourceSpecies: Unidentified

Experimental details

Sample preparation

Specimen statefilament
Helical parametersHand: RIGHT HANDED / Delta z: 24.2 Å / Delta phi: 165 deg.
VitrificationInstrument: NONE / Cryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: 626 / Model: GATAN LIQUID NITROGEN

Image processing

ProcessingMethod: helical reconstruction

Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 1MWK
Output model

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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)

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