3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome
by single particle reconstruction, at 10.8 A resolution
#1: Depositted structure unit, Made by Jmol
#2: Superimposing with simplified surface model of EM map, EMDB-1055, Made by Jmol
#3: Superimposing with simplified surface model of EM map, EMDB-1362, Made by Jmol
#4: Superimposing with simplified surface model of EM map, EMDB-1363, Made by Jmol
#5: Superimposing with simplified surface model of EM map, EMDB-1365, Made by Jmol
#6: Superimposing with simplified surface model of EM map, EMDB-1366, Made by Jmol
#7: With PDB-1pn6, PDB-1pn8, Made by Jmol
#8: Superimposing with EM 3D map: EMDB-1055 (with PDB-1pn6, PDB-1pn8), Made by UCSF CHIMERA
#9: Superimposing with EM 3D map: EMDB-1363 (with PDB-1pn6, PDB-1pn8), Made by UCSF CHIMERA
#10: Superimposing with EM 3D map: EMDB-1365 (with PDB-1pn6, PDB-1pn8), Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 1pn7 |
|---|---|
| Title | Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome |
| Descriptor | RNA BINDING PROTEIN/RNA Complex |
| Keywords |  RNA binding protein/RNA, ribosomal protein, tRNA binding protein, tRNA, RNA binding protein-RNA COMPLEX |
| Authors | Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M., Frank, J. |
| Date | Deposition: 2003-06-12, Release: 2003-07-15 |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Structure Visualization | |
| Movies |  Movie Page#1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-1055, Made by Jmol #3: Superimposing with simplified surface model of EM map, EMDB-1362, Made by Jmol #4: Superimposing with simplified surface model of EM map, EMDB-1363, Made by Jmol #5: Superimposing with simplified surface model of EM map, EMDB-1365, Made by Jmol #6: Superimposing with simplified surface model of EM map, EMDB-1366, Made by Jmol #7: With PDB-1pn6, PDB-1pn8, Made by Jmol #8: Superimposing with EM 3D map: EMDB-1055 (with PDB-1pn6, PDB-1pn8), Made by UCSF CHIMERA #9: Superimposing with EM 3D map: EMDB-1363 (with PDB-1pn6, PDB-1pn8), Made by UCSF CHIMERA #10: Superimposing with EM 3D map: EMDB-1365 (with PDB-1pn6, PDB-1pn8), Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | Cell, Vol. 114, Issue 1, Page 123-34, Year 2003 |
|---|---|
| Title | Locking and unlocking of ribosomal motions. |
| Authors | Mikel Valle, Andrey Zavialov, Jayati Sengupta, Urmila Rawat, Måns Ehrenberg, Joachim Frank Howard Hughes Medical Institute, and Health Research Incororated at the Wadswoth Center, State University of New York, Albany, 12201, USA. |
| Keywords | Binding Sites (genetics), Cryoelectron Microscopy, Eukaryotic Cells (metabolism), Models, Molecular, Molecular Conformation, Peptide Elongation Factor G (genetics), Peptides (genetics), Protein Biosynthesis (genetics), Protein Structure, Tertiary (genetics), Protein Subunits (genetics), RNA, Messenger (genetics), RNA, Transfer (genetics, 9014-25-9), Ribosomes (genetics), Rotation |
| Links | PubMed: 12859903, PII: S0092867403004768 |
 Components | |
| ID 1 : P-tRNA | |
| Image |   |
|---|---|
| Description | P-tRNA |
| Type | polymer |
| Formula weight | 20017.092 Da |
| Number of molecules | 1 |
| Source | Method: Obtained synthetically |
| Links | Sequence view |
| ID 2 : 30S ribosomal protein S12 | |
| Image |   |
| Description | 30S ribosomal protein S12 |
| Type | polymer |
| Formula weight | 13804.441 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Thermus NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SHN3, Sequence view |
| ID 3 : 50S ribosomal protein L11 | |
| Image |   |
| Description | 50S ribosomal protein L11 |
| Type | polymer |
| Formula weight | 14295.032 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Thermotoga NCBI taxonomy: ID:2336Organism scientific: Thermotoga maritima |
| Links | UniProt: P29395, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Entity assembly | |
| Name | P-tRNA |
| Entity assembly | |
| GO-ID | GO:0006412 |
| InterPro-ID | IPR:006032 |
| Name | 30S ribosomal protein S12 |
| Entity assembly | |
| GO-ID | GO:0006412 |
| InterPro-ID | IPR:000911 |
| Name | 50S ribosomal protein L11 |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 7.5 |
| Sample concentration | 32 mg/ml |
| Sample support | |
| Details | Quantifoil holley-carbon film grids |
| Vitrification | |
| Details | Rapid-freezing in liquid ethane |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: FEI TECNAI F20 |
|---|---|
| Date | 2001-06-01 |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 200 kV |
| Electron dose | 2000 e/A**2 |
| Illumination mode | FLOOD BEAM |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | calibrated: 49696 X, nominal: 50000 X |
| Cs | nominal: 2.0 mm |
| Nominal defocus | max: 4000. nm, min: 1500. nm |
| Specimen holder | |
| Tilt angle | min: 0 degrees, max: 0 degrees |
| Temperature | 93 Kelvin |
| Detector | |
| Type | KODAK SO163 FILM |
 Processing | |
| Single particle entity | |
| Symmetry type | ASYMMETRIC |
|---|---|
| 3D reconstruction | |
| Actual pixel size | 2.82 A/pix |
| CTF correction method | CTF correction of 3D-maps by Wiener filtration |
| Details | SPIDER package. Crystal Structure of Thermus Thermophilus 70S ribosome |
| Magnification calibration | TMV |
| Method | 3D projection matching; conjugate gradients with regularization |
| Resolution | 10.8 A |
| 3D fitting | |
| Method | Manual fitting in O |
| Refinement Space | REAL |
| Refine hist | |
| Total atoms | 319 |
| Nucleic acid atoms | 62 |
| Protein atoms | 257 |
Top
Gallery
List
Diagram
Statistics
Documents
PDBj
EM Navigator
Detail page - PDB-1pn7
Download
Contact