3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Structure of the 30S subunit of a pre-translocational E. coli ribosome obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1056
by single particle reconstruction, at 15 A resolution
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 2gy9 |
|---|---|
| Title | Structure of the 30S subunit of a pre-translocational E. coli ribosome obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1056 |
| Descriptor | 30S RIBOSOMAL SUBUNIT |
| Keywords |  RIBOSOME, SecM, nascent chain, signal transduction, RNA world, polypeptide exit tunnel, translocation, ribosome, elongation arrest |
| Authors | Mitra, K., Frank, J. |
| Date | Deposition: 2006-05-09, Release: 2006-09-26 |
| 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-1056, Made by Jmol #3: With PDB-2gya, Made by Jmol #4: Superimposing with EM 3D map: EMDB-1056 (with PDB-2gya), 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 Split: split data constructing the same model |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | Mol. Cell, Vol. 22, Issue 4, Page 533-43, Year 2006 |
|---|---|
| Title | Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements. |
| Authors | Kakoli Mitra, Christiane Schaffitzel, Felcy Fabiola, Michael S Chapman, Nenad Ban, Joachim Frank Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, Empire State Plaza, Albany, New York 12201, USA. |
| Keywords | Cryoelectron Microscopy, Escherichia coli (genetics), Escherichia coli Proteins (chemistry), Macromolecular Substances, Models, Molecular, Nucleic Acid Conformation, Peptide Chain Elongation, Translational, Protein Conformation, RNA, Bacterial (chemistry), RNA, Ribosomal (chemistry), RNA, Ribosomal, 23S (chemistry), Ribosomes (metabolism), SecM protein, E coli, Transcription Factors (chemistry) |
| Links | PII: S1097-2765(06)00294-2, DOI: 10.1016/j.molcel.2006.05.003, PubMed: 16713583 |
| Citation - 1 | |
| Article | Nature, Vol. 438, Page: 318 - 324, Year: 2005, |
| Title | Structure of the E. coli protein-conducting channel bound to a translating ribosome |
| Authors | Mitra, K., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks III, C.L., Ban, N., Frank, J. |
| Citation - 2 | |
| Article | Cell(Cambridge,Mass.), Vol. 114, Page: 123 - 134, Year: 2003, |
| Title | Locking and unlocking of ribosomal motions |
| Authors | Valle, M., Zavialov, A.V., Sengupta, J., Rawat, U., Ehrenberg, M., Frank, J. |
| Citation - 3 | |
| Article | FEBS Lett., Vol. 580, Issue 14, Page 3353-60, Year 2006 |
| Title | A model for co-translational translocation: ribosome-regulated nascent polypeptide translocation at the protein-conducting channel. |
| Authors | Kakoli Mitra, Joachim Frank Howard Hughes Medical Institute, Health Research, Inc. at the Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA. |
| Keywords | Models, Molecular, Protein Biosynthesis, Protein Conformation, Protein Transport, Ribosomes (metabolism) |
| Links | PII: S0014-5793(06)00609-0, DOI: 10.1016/j.febslet.2006.05.019, PubMed: 16714018 |
 Components | |
| ID 1 : 16S ribosomal RNA | |
| Image |   |
|---|---|
| Description | 16S ribosomal RNA |
| Type | polymer |
| Formula weight | 482286.844 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli
|
| Links | Sequence view |
| ID 2 : tRNA | |
| Image |   |
| Description | tRNA |
| Type | polymer |
| Formula weight | 24518.730 Da |
| Number of molecules | 3 |
| Details | A-site, P-site, E-site |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | Sequence view |
| ID 3 : 30S ribosomal subunit protein S2 | |
| Image |   |
| Description | 30S ribosomal subunit protein S2 |
| Type | polymer |
| Formula weight | 26292.264 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7V0, Sequence view |
| ID 4 : 30S ribosomal subunit protein S3 | |
| Image |   |
| Description | 30S ribosomal subunit protein S3 |
| Type | polymer |
| Formula weight | 23078.988 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7V3, Sequence view |
| ID 5 : 30S ribosomal subunit protein S4 | |
| Image |   |
| Description | 30S ribosomal subunit protein S4 |
| Type | polymer |
| Formula weight | 23312.113 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7V8, Sequence view |
| ID 6 : 30S ribosomal subunit protein S5 | |
| Image |   |
| Description | 30S ribosomal subunit protein S5 |
| Type | polymer |
| Formula weight | 15618.174 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7W1, Sequence view |
| ID 7 : 30S ribosomal subunit protein S6 | |
| Image |   |
| Description | 30S ribosomal subunit protein S6 |
| Type | polymer |
| Formula weight | 11181.960 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P02358, Sequence view |
| ID 8 : 30S ribosomal subunit protein S7 | |
| Image |   |
| Description | 30S ribosomal subunit protein S7 |
| Type | polymer |
| Formula weight | 15384.802 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P02359, Sequence view |
| ID 9 : 30S ribosomal subunit protein S8 | |
| Image |   |
| Description | 30S ribosomal subunit protein S8 |
| Type | polymer |
| Formula weight | 13857.312 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7W7, Sequence view |
| ID 10 : 30S ribosomal subunit protein S9 | |
| Image |   |
| Description | 30S ribosomal subunit protein S9 |
| Type | polymer |
| Formula weight | 14440.900 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7X3, Sequence view |
| ID 11 : 30S ribosomal subunit protein S10 | |
| Image |   |
| Description | 30S ribosomal subunit protein S10 |
| Type | polymer |
| Formula weight | 10996.862 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7R5, Sequence view |
| ID 12 : 30S ribosomal subunit protein S11 | |
| Image |   |
| Description | 30S ribosomal subunit protein S11 |
| Type | polymer |
| Formula weight | 12388.177 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7R9, Sequence view |
| ID 13 : 30S ribosomal subunit protein S12 | |
| Image |   |
| Description | 30S ribosomal subunit protein S12 |
| Type | polymer |
| Formula weight | 11245.187 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7S3, Sequence view |
| ID 14 : 30S ribosomal subunit protein S13 | |
| Image |   |
| Description | 30S ribosomal subunit protein S13 |
| Type | polymer |
| Formula weight | 12739.017 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7S9, Sequence view |
| ID 15 : 30S ribosomal subunit protein S14 | |
| Image |   |
| Description | 30S ribosomal subunit protein S14 |
| Type | polymer |
| Formula weight | 7117.417 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG59, Sequence view |
| ID 16 : 30S ribosomal subunit protein S15 | |
| Image |   |
| Description | 30S ribosomal subunit protein S15 |
| Type | polymer |
| Formula weight | 9915.440 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0ADZ4, Sequence view |
| ID 17 : 30S ribosomal subunit protein S16 | |
| Image |   |
| Description | 30S ribosomal subunit protein S16 |
| Type | polymer |
| Formula weight | 8822.221 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7T3, Sequence view |
| ID 18 : 30S ribosomal subunit protein S17 | |
| Image |   |
| Description | 30S ribosomal subunit protein S17 |
| Type | polymer |
| Formula weight | 9134.845 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG63, Sequence view |
| ID 19 : 30S ribosomal subunit protein S18 | |
| Image |   |
| Description | 30S ribosomal subunit protein S18 |
| Type | polymer |
| Formula weight | 8178.542 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7T7, Sequence view |
| ID 20 : 30S ribosomal subunit protein S19 | |
| Image |   |
| Description | 30S ribosomal subunit protein S19 |
| Type | polymer |
| Formula weight | 9865.638 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7U3, Sequence view |
| ID 21 : 30S ribosomal subunit protein S20 | |
| Image |   |
| Description | 30S ribosomal subunit protein S20 |
| Type | polymer |
| Formula weight | 9279.014 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7U7, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000851 |
| Name | 30S ribosomal protein S2 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0005840 |
| InterPro-ID | IPR:008282 |
| Name | 30S ribosomal subunit protein S3 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005709 |
| Name | 30S ribosomal subunit protein S4 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000851 |
| Name | 30S ribosomal subunit protein S5 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000529 |
| Name | 30S ribosomal subunit protein S6 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005717 |
| Name | 30S ribosomal subunit protein S7 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000630 |
| Name | 30S ribosomal subunit protein S8 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000754 |
| Name | 30S ribosomal subunit protein S9 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005731 |
| Name | 30S ribosomal subunit protein S10 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001971 |
| Name | 30S ribosomal subunit protein S11 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005679 |
| Name | 30S ribosomal subunit protein S12 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001892 |
| Name | 30S ribosomal subunit protein S13 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001209 |
| Name | 30S ribosomal subunit protein S14 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005290 |
| Name | 30S ribosomal subunit protein S15 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000307 |
| Name | 30S ribosomal subunit protein S16 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000266 |
| Name | 30S ribosomal subunit protein S17 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001648 |
| Name | 30S ribosomal subunit protein S18 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005732 |
| Name | 30S ribosomal subunit protein S19 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:002583 |
| Name | 30S ribosomal subunit protein S20 |
| 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 holey-Carbon film grids |
| Vitrification | |
| Details | rapid-freezing in liquid ethane |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: FEI TECNAI F20 |
|---|---|
| Date | 2002-07-01 |
| 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: 3.8 nm, min: 1.1 nm |
| Specimen holder | |
| Tilt angle | min: 0 degrees, max: 0 degrees |
| Temperature | 93 Kelvin |
| Detector | |
| Type | KODAK SO163 film |
 Processing | |
| 2D projection selection | |
| Software name | CNS implementation of RSRef |
|---|---|
| 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 | WITH THE USE OF APPROPRIATE STEREOCHEMICAL CONSTRAINTS, AN ATOMIC MODEL FITTED INTO AN EM MAP YIELDS AN ACCURACY OF 5-FOLD BETTER THAN THE NOMINAL RESOLUTION OF THE EM MAP. THE RESOLUTION OF THE ATOMIC MODEL FITTED INTO EMD-1056 (NOMINAL RESOLUTION 15.0 ANGSTROMS) IS THUS ESTIMATED TO BE BETWEEN 2-3 ANGSTROMS. REAL-SPACE REFINEMENT USING RIGID BODIES INTO EM MAP EMD-1056 (FILTERED TO A NOMINAL RESOLUTION OF 15 ANGSTROMS). RIGID BODY DEFINITION: AN AUTONOMOUS SECONDARY STRUCTURE UNIT (E.G. HELIX SEGMENT, HAIRPIN) OF THE RIBOSOMAL RNA; AN AUTONOMOUS RIBOSOMAL PROTEIN DOMAIN. THE ATOMIC MODEL USED WAS GENERATED FROM E. COLI MODELS OF X-RAY CRYSTALLOGRAPHY STRUCTURES OF RIBOSOMES FROM OTHER ORGANISMS. IN THE ABSENCE OF E. COLI MODELS, STRUCTURES WERE DERIVED DIRECTLY FROM THE X-RAY CRYSTALLOGRAPHY STRUCTURES OF RIBOSOMES FROM OTHER ORGANISMS. |
| Magnification calibration | TMV |
| Method | 3D projection matching; conjugate gradients with regularization |
| Nominal pixel size | 2.82 A/pix |
| Resolution | 15 A |
| 3D fitting | |
| Refinement Protocol | CNS implementation of RSRef |
| Refinement Space | REAL |
| Software name | CNS implementation of RSRef |
| Target criteria | Minimization of number of poor van der Waals contacts and maximation of correlation coefficient |
| Refine hist | |
| Total atoms | 54539 |
| Nucleic acid atoms | 36790 |
| Protein atoms | 17749 |
 Download | |||
| PDB format | |||
| All | pdb2gy9.ent.gzpdb2gy9.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb2gy9.ent.gz | ||
| mmCIF format | |||
| mmCIF | 2gy9.cif.gz | ||
| XML format | |||
| All | 2gy9.xml.gz | ||
| No-atom | 2gy9-noatom.xml.gz | ||
| Ext-atom | 2gy9-extatom.xml.gz | ||
| Movie files | |||
| movie #1 |
| ||
| movie #2 |
| ||
| movie #3 |
| ||
| movie #4 |
| ||
Top
Gallery
List
Diagram
Statistics
Documents
PDBj
EM Navigator
Detail page - PDB-2gy9
Contact