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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
#1: Surface view with section colored by density value, Surface level: 9.0672E-5, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 9.0672E-5, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1470 |
|---|---|
| Title | Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability |
| Map | A volume file of ParM filament |
| Sample | ParM filament |
| Keywords |  GTPase, molecular switch, filament, ParM |
| Authors | Popp D, Narita A, Oda T, Fujisawa T, Matsuo H, Nitanai Y, Iwasa M, Maeda K, Onishi H, Maeda Y |
| Date | Deposition: 2008-02-14, Header release: 2008-02-19, Map release: 2009-03-31, Last update: 2012-10-24 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 9.0672E-5, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 9.0672E-5, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | EMBO J., Vol. 27, Issue 3, Page 570-9, 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 ERATO Actin Filament Dynamics Project, RIKEN Harima Institute, Japan Science and Technology Corporation, Sayo, Hyogo, Japan. |
| Keywords | Actins (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 |
| Links | DOI: 10.1038/sj.emboj.7601978, PubMed: 18188150, PMC: PMC2241650 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1470.map ( map file in CCP4 format, 270 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A: 160.44 A, B: 160.44 A, C: 168.462 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 4.011 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | A volume file of ParM filament | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | ParM filament |
|---|---|
| Number of Components | 1 |
| Oligomeric State | Filament |
| Theoretical Mass | 0.035MDa |
| Component #1: protein - ParM | |
| Scientific name | ParM |
| Oligomeric Details | Helical filament |
| Number of Copies | 10 |
| Scientific Name of Species | Escherichia coli
|
| NCBI taxonomy | 562 |
| Recombinant expression | Yes |
| Engineered Source | NCBI taxonomy: 562 Expression system: Escherichia coli |
 Experiment | |
| Sample Preparation | |
| Helical Parameters | Hand: LEFT HANDED |
|---|---|
| Staining | 1.0 % uranyl acetate |
| Specimen Conc | 0.14 mg/ml |
| Specimen State | filament |
| Buffer | pH: 7.5 Details: 10 mM Hepes, 25 mM KCl, 1 mM MgCl2, 1 mM DTT, 5 mM GMPPNP |
| Vitrification | |
| Cryogen Name | NONE |
| Instrument | NONE |
| Imaging | |
| Microscope | OTHER |
| Electron Gun | |
| Electron Source | LAB6 |
| Accelerating Voltage | 100 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Model | OTHER |
| Camera | |
| Image Acquisition | |
| Number of Digital Images | 7 |
| Sampling Size | 7 |
 Processing | |
| Method | helical reconstruction |
|---|---|
| 3D reconstruction | |
| Software | EOS |
| CTF Correction | Each filament |
| Resolution By Author | 23 A |
| Resolution Method | FSC at 0.5 cut-off |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: Rigid body. After rigid body fitting the structure was refined by energy minimization with program NAMD |
| Software | situs |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| PDB Entry ID | 1MWM |
| PDB Chain ID | 1MWM_A |
| Fitted Coordinate | |
| PDB entry ID | |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1470.xml (6.6 KB) | ||
|---|---|---|---|
| Map data | emd_1470.map.gz (196.2 KB) | ||
| Images |  1470.gif (29.6 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1470 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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