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Lidless Mm-cpn in the open state
by single particle reconstruction, at 8 A resolution
#1: Surface view colored by cylindrical radius, Surface level: 1.05, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 1.05, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-3iyf, Surface level: 1.05, Made by UCSF CHIMERA
#4: Surface view with fitted model, atomic models: PDB-3iyf, Surface level: 1.05, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5140 |
|---|---|
| Authors | Zhang J, Baker ML, Schroeder G, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view colored by cylindrical radius, Surface level: 1.05, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 1.05, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3iyf, Surface level: 1.05, Made by UCSF CHIMERA #4: Surface view with fitted model, atomic models: PDB-3iyf, Surface level: 1.05, 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 | Nature, Vol. 463, Issue 7279, Page 379-83, Year 2010 |
|---|---|
| Title | Mechanism of folding chamber closure in a group II chaperonin. |
| Authors | Junjie Zhang, Matthew L Baker, Gunnar F Schröder, Nicholai R Douglas, Stefanie Reissmann, Joanita Jakana, Matthew Dougherty, Caroline J Fu, Michael Levitt, Steven J Ludtke, Judith Frydman, Wah Chiu Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA. |
| Keywords |  Adenosine Triphosphate (chemistry, 56-65-5), Allosteric Regulation, Binding Sites, Cryoelectron Microscopy, Group II Chaperonins (chemistry, 3.6.1.-), Hydrolysis (drug effects), Methanococcus (chemistry), Models, Molecular, Protein Binding, Protein Conformation (drug effects), Protein Folding, Protein Subunits (chemistry), Structure-Activity Relationship |
| Links | DOI: 10.1038/nature08701, PubMed: 20090755, PMC: PMC2834796 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5140.map ( map file in CCP4 format, 55298 KB ) | ||||||||||||||||||||||||
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| 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 = 319.2 A , B = 319.2 A , C = 319.2 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1.33 A , Y = 1.33 A , Z = 1.33 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is a map of the lidless Mm-cpn in the nucleotide-free open state. | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Lidless Mm-cpn |
|---|---|
| Number of Components | 1 |
| Oligomeric State | 16-mer |
| Theoretical Mass | 0.96 MDa |
| Experimental Mass | 0.96 MDa |
| Component #1: protein - Lidless Mm-cpn | |
| Scientific name | Lidless Methanococcus maripaludis chaperonin |
| Common Name | Lidless Mm-cpn |
| Theoretical Mass | 0.96 MDa |
| Experimental Mass | 0.96 MDa |
| Oligomeric Details | 16-mer |
| Number of Copies | 16 |
| Scientific Name of Species | Methanococcus maripaludis (NCBI Taxonomy: 39152) |
| Recombinant expression | Yes |
| Engineered Source | Exp System: Escherichia coli (NCBI Taxonomy: 562) |
 Experiment | |
| Sample Preparation | |
| Specimen State | particle |
|---|---|
| Vitrification | |
| Method | 1 blot 3 seconds |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Imaging | |
| Microscope | JEOL 3200FSC |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 80000 X, Calibrated: 112000 X |
| Astigmatism | objective lens astigmatism was corrected at 100,000 times magnification |
| Nominal Cs | 4.1 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1000 nm - 3000 nm |
| Energy Filter | Type: in column omega filter , Window: 0-10 eV |
| Specimen Holder | |
| Holder | side-entry ( JEOL 3200FSC CRYOHOLDER ) |
| Temperature | 100 Kelvin |
| Camera | |
| Detector | Gatan 4kX4k CCD Camera |
| Image Acquisition | |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Projection-match |
| Software | EMAN |
| CTF Correction | Each micrograph |
| Resolution By Author | 8 |
| Resolution Method | FSC at 0.5 cut-off |
| Fitted Coordinate | |
| PDB entry ID | |
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