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Lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state
by single particle reconstruction, at 8 A resolution
#1: Surface view with section colored by density value, Surface level: 0.075, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 0.075, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-3j02, Surface level: 0.075, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5258 |
|---|---|
| Title | Lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state |
| Map | This is the density map of lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state. |
| Sample | Lidless D386A Mm-cpn variant |
| Keywords |  Mm-cpn, Chaperonin, ATP-bound |
| Authors | Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak L, Baker D, Frydman J, Levitt M, Chiu W |
| Date | Deposition: 2011-02-10, Header release: 2011-05-11, Map release: 2011-05-11, Last update: 2011-05-11 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.075, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.075, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3j02, Surface level: 0.075, 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 | Structure, Vol. 19, Issue 5, Page 633-9, Year 2011 |
|---|---|
| Title | Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure. |
| Authors | Junjie Zhang, Boxue Ma, Frank DiMaio, Nicholai R Douglas, Lukasz A Joachimiak, David Baker, Judith Frydman, Michael Levitt, Wah Chiu Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA. |
| Keywords | Adenosine Triphosphate (metabolism, 56-65-5), Binding Sites, Cryoelectron Microscopy (methods), Group II Chaperonins (chemistry, 3.6.1.-), Hydrolysis, Methanococcus (chemistry), Models, Molecular, Protein Binding, Protein Conformation, Protein Folding, Protein Subunits (chemistry) |
| Links | PII: S0969-2126(11)00102-X, DOI: 10.1016/j.str.2011.03.005, PubMed: 21565698 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5258.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 = 340.8 A , B = 340.8 A , C = 340.8 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1.42 A , Y = 1.42 A , Z = 1.42 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is the density map of lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state. | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Lidless D386A Mm-cpn variant |
|---|---|
| Number of Components | 1 |
| Theoretical Mass | 1 MDa |
| Experimental Mass | 1 MDa |
| Component #1: protein - Mm-cpn | |
| Scientific name | Methanococcus maripaludis chaperonin |
| Common Name | Mm-cpn |
| Theoretical Mass | 1 MDa |
| Experimental Mass | 1 MDa |
| Details | incubated with 1mM ATP |
| Oligomeric Details | 16-mer |
| Number of Copies | 1 |
| 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 | |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: vitrobot |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Imaging | |
| Microscope | JEOL 2200FS |
| Date | 08-SEP-2009 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 80000 X, Calibrated: 112000 X |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1000 nm - 2500 nm |
| Energy Filter | Type: in-column omega energy filter , Window: 0-10 eV |
| Specimen Holder | |
| Holder | Gatan side entry ( GATAN LIQUID NITROGEN ) |
| Camera | |
| Detector | Gatan 4Kx4K CCD camera |
| Image Acquisition | |
| Number of Digital Images | 64 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | projection matching |
| Software | EMAN |
| CTF Correction | Each CCD image |
| Resolution By Author | 8 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 12761 |
| Fitted Coordinate | |
| PDB entry ID | |
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