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Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability

by helical reconstruction, at 23 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 9.0672E-5, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 9.0672E-5, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1470
TitleMolecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability
MapA volume file of ParM filament
SampleParM filament
KeywordsGTPase, molecular switch, filament, ParM
AuthorsPopp D, Narita A, Oda T, Fujisawa T, Matsuo H, Nitanai Y, Iwasa M, Maeda K, Onishi H, Maeda Y
DateDeposition: 2008-02-14, Header release: 2008-02-19, Map release: 2009-03-31, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 9.0672E-5, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 9.0672E-5, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
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CiteFit

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List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 27, Issue 3, Page 570-9, Year 2008
TitleMolecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability.
AuthorsDavid Popp, Akihiro Narita, Toshiro Oda, Tetsuro Fujisawa, Hiroshi Matsuo, Yasushi Nitanai, Mitsusada Iwasa, Kayo Maeda, Hirofumi Onishi, Yuichiro Maéda
ERATO Actin Filament Dynamics Project, RIKEN Harima Institute, Japan Science and Technology Corporation, Sayo, Hyogo, Japan.
KeywordsActins (chemistry), Crystallography, X-Ray, Cytoskeleton (chemistry), DNA, Bacterial (physiology), Escherichia coli (chemistry), Escherichia coli Proteins (chemistry), GTP-Binding Proteins (chemistry, 3.6.1.-), Nucleotides (physiology), ParM protein, E coli, Protein Binding (physiology), Protein Structure, Quaternary, Protein Structure, Tertiary, Thermodynamics
LinksDOI: 10.1038/sj.emboj.7601978, PubMed: 18188150, PMC: PMC2241650
Map
Fileemd_1470.map.gz ( map file in CCP4 format, 264 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
42 pix
4.011 A/pix
= 168.462 A
40 pix
4.011 A/pix
= 160.44 A
40 pix
4.011 A/pix
= 160.44 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
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)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions404042
Origin000
Limit393941
Spacing404042
Unit CellA: 160.44 A, B: 160.44 A, C: 168.462 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.011 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS404042
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0000.0000.000
Annotation DetailsA volume file of ParM filament
Supplement
Images
Images
Sample
NameParM filament
Number of Components1
Oligomeric StateFilament
Theoretical Mass0.035MDa
Component #1: protein - ParM
Scientific nameParM
Oligomeric DetailsHelical filament
Number of Copies10
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Helical ParametersHand: LEFT HANDED
Staining1.0 % uranyl acetate
Specimen Conc0.14 mg/ml
Specimen Statefilament
BufferpH: 7.5
Details: 10 mM Hepes, 25 mM KCl, 1 mM MgCl2, 1 mM DTT, 5 mM GMPPNP
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 2010HC
Electron Gun
Electron SourceLAB6
Accelerating Voltage100 kV
Illumination ModeFLOOD BEAM
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelOTHER
Camera
Image Acquisition
Number of Digital Images7
Sampling Size7
Processing
Methodhelical reconstruction
3D reconstruction
SoftwareEOS
CTF CorrectionEach filament
Resolution By Author23 A
Resolution MethodFSC 0.5
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid body. After rigid body fitting the structure was refined by energy minimization with program NAMD
Softwaresitus
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID1MWM
PDB Chain ID1MWM_A
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1470.xml (6.6 KB)
Map dataemd_1470.map.gz (196.2 KB)
Images1470.gif (29.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1470
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 20 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 20.1 KB