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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 |
| 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 |
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, Page: 533 - 543, Year: 2006, |
|---|---|
| Title | Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements |
| Authors | Mitra, K., Schaffitzel, C., Fabiola, F., Chapman, M.S., Ban, N., Frank, J. |
| Links | DOI: 10.1016/j.molcel.2006.05.003 |
| 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 | polyribonucleotide |
| Formula weight | 482286.844 Da |
| Number of molecules | 1 |
| ID | 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 | polyribonucleotide |
| Formula weight | 24518.730 Da |
| Number of molecules | 3 |
| ID | 2 |
| 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 | polypeptide(L) |
| Formula weight | 26292.264 Da |
| Number of molecules | 1 |
| ID | 3 |
| 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 | polypeptide(L) |
| Formula weight | 23078.988 Da |
| Number of molecules | 1 |
| ID | 4 |
| 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 | polypeptide(L) |
| Formula weight | 23312.113 Da |
| Number of molecules | 1 |
| ID | 5 |
| 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 | polypeptide(L) |
| Formula weight | 15618.174 Da |
| Number of molecules | 1 |
| ID | 6 |
| 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 | polypeptide(L) |
| Formula weight | 11181.960 Da |
| Number of molecules | 1 |
| ID | 7 |
| 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 | polypeptide(L) |
| Formula weight | 15384.802 Da |
| Number of molecules | 1 |
| ID | 8 |
| 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 | polypeptide(L) |
| Formula weight | 13857.312 Da |
| Number of molecules | 1 |
| ID | 9 |
| 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 | polypeptide(L) |
| Formula weight | 14440.900 Da |
| Number of molecules | 1 |
| ID | 10 |
| 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 | polypeptide(L) |
| Formula weight | 10996.862 Da |
| Number of molecules | 1 |
| ID | 11 |
| 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 | polypeptide(L) |
| Formula weight | 12388.177 Da |
| Number of molecules | 1 |
| ID | 12 |
| 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 | polypeptide(L) |
| Formula weight | 11245.187 Da |
| Number of molecules | 1 |
| ID | 13 |
| 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 | polypeptide(L) |
| Formula weight | 12739.017 Da |
| Number of molecules | 1 |
| ID | 14 |
| 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 | polypeptide(L) |
| Formula weight | 7117.417 Da |
| Number of molecules | 1 |
| ID | 15 |
| 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 | polypeptide(L) |
| Formula weight | 9915.440 Da |
| Number of molecules | 1 |
| ID | 16 |
| 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 | polypeptide(L) |
| Formula weight | 8822.221 Da |
| Number of molecules | 1 |
| ID | 17 |
| 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 | polypeptide(L) |
| Formula weight | 9134.845 Da |
| Number of molecules | 1 |
| ID | 18 |
| 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 | polypeptide(L) |
| Formula weight | 8178.542 Da |
| Number of molecules | 1 |
| ID | 19 |
| 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 | polypeptide(L) |
| Formula weight | 9865.638 Da |
| Number of molecules | 1 |
| ID | 20 |
| 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 | polypeptide(L) |
| Formula weight | 9279.014 Da |
| Number of molecules | 1 |
| ID | 21 |
| 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 | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000851 |
| Name | 30S ribosomal protein S2 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0005840 |
| InterPro-ID | IPR:008282 |
| Name | 30S ribosomal subunit protein S3 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005709 |
| Name | 30S ribosomal subunit protein S4 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000851 |
| Name | 30S ribosomal subunit protein S5 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000529 |
| Name | 30S ribosomal subunit protein S6 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005717 |
| Name | 30S ribosomal subunit protein S7 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000630 |
| Name | 30S ribosomal subunit protein S8 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000754 |
| Name | 30S ribosomal subunit protein S9 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005731 |
| Name | 30S ribosomal subunit protein S10 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001971 |
| Name | 30S ribosomal subunit protein S11 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005679 |
| Name | 30S ribosomal subunit protein S12 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001892 |
| Name | 30S ribosomal subunit protein S13 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001209 |
| Name | 30S ribosomal subunit protein S14 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005290 |
| Name | 30S ribosomal subunit protein S15 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000307 |
| Name | 30S ribosomal subunit protein S16 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000266 |
| Name | 30S ribosomal subunit protein S17 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001648 |
| Name | 30S ribosomal subunit protein S18 |
| Entity assembly | |
| Assembly-ID | 1 |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005732 |
| Name | 30S ribosomal subunit protein S19 |
| Entity assembly | |
| Assembly-ID | 1 |
| 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 |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
 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 | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| 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 |
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| movie #2 |
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| movie #4 |
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