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Structure of the 50S 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) / 2gya |
|---|---|
| Title | Structure of the 50S 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 | 50S 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-2gy9, Made by Jmol #4: Superimposing with EM 3D map: EMDB-1056 (with PDB-2gy9), 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 : 23S ribosomal RNA | |
| Image |   |
|---|---|
| Description | 23S ribosomal RNA |
| Type | polymer |
| Formula weight | 888504.688 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 : 5S ribosomal RNA | |
| Image |   |
| Description | 5S ribosomal RNA |
| Type | polymer |
| Formula weight | 34917.012 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 3 : 50S ribosomal protein L1 | |
| Image |   |
| Description | 50S ribosomal protein L1 |
| Type | polymer |
| Formula weight | 23591.438 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7L0, Sequence view |
| ID 4 : 50S ribosomal protein L7/L12 | |
| Image |   |
| Description | 50S ribosomal protein L7/L12 |
| Type | polymer |
| Formula weight | 12090.999 Da |
| Number of molecules | 2 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7K2, Sequence view |
| ID 5 : 50S ribosomal protein L2 | |
| Image |   |
| Description | 50S ribosomal protein L2 |
| Type | polymer |
| Formula weight | 24691.438 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60422, Sequence view |
| ID 6 : 50S ribosomal protein L3 | |
| Image |   |
| Description | 50S ribosomal protein L3 |
| Type | polymer |
| Formula weight | 22277.709 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60438, Sequence view |
| ID 7 : 50S ribosomal protein L4 | |
| Image |   |
| Description | 50S ribosomal protein L4 |
| Type | polymer |
| Formula weight | 21806.293 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60723, Sequence view |
| ID 8 : 50S ribosomal protein L5 | |
| Image |   |
| Description | 50S ribosomal protein L5 |
| Type | polymer |
| Formula weight | 20131.486 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P62399, Sequence view |
| ID 9 : 50S ribosomal protein L6 | |
| Image |   |
| Description | 50S ribosomal protein L6 |
| Type | polymer |
| Formula weight | 17799.543 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG55, Sequence view |
| ID 10 : 50S ribosomal protein L9 | |
| Image |   |
| Description | 50S ribosomal protein L9 |
| Type | polymer |
| Formula weight | 15789.174 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7R1, Sequence view |
| ID 11 : 50S ribosomal protein L11 | |
| Image |   |
| Description | 50S ribosomal protein L11 |
| Type | polymer |
| Formula weight | 14577.119 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7J7, Sequence view |
| ID 12 : 50S ribosomal protein L13 | |
| Image |   |
| Description | 50S ribosomal protein L13 |
| Type | polymer |
| Formula weight | 16050.749 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AA10, Sequence view |
| ID 13 : 50S ribosomal protein L14 | |
| Image |   |
| Description | 50S ribosomal protein L14 |
| Type | polymer |
| Formula weight | 13433.980 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0ADY3, Sequence view |
| ID 14 : 50S ribosomal protein L15 | |
| Image |   |
| Description | 50S ribosomal protein L15 |
| Type | polymer |
| Formula weight | 14477.937 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P02413, Sequence view |
| ID 15 : 50S ribosomal protein L16 | |
| Image |   |
| Description | 50S ribosomal protein L16 |
| Type | polymer |
| Formula weight | 14736.614 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0ADY7, Sequence view |
| ID 16 : 50S ribosomal protein L17 | |
| Image |   |
| Description | 50S ribosomal protein L17 |
| Type | polymer |
| Formula weight | 12945.183 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG44, Sequence view |
| ID 17 : 50S ribosomal protein L18 | |
| Image |   |
| Description | 50S ribosomal protein L18 |
| Type | polymer |
| Formula weight | 12273.206 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0C018, Sequence view |
| ID 18 : 50S ribosomal protein L19 | |
| Image |   |
| Description | 50S ribosomal protein L19 |
| Type | polymer |
| Formula weight | 13028.207 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7K6, Sequence view |
| ID 19 : 50S RIBOSOMAL PROTEIN L20 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L20 |
| Type | polymer |
| Formula weight | 13254.805 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7L3, Sequence view |
| ID 20 : 50S ribosomal protein L22 | |
| Image |   |
| Description | 50S ribosomal protein L22 |
| Type | polymer |
| Formula weight | 11778.894 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P61175, Sequence view |
| ID 21 : 50S ribosomal protein L23 | |
| Image |   |
| Description | 50S ribosomal protein L23 |
| Type | polymer |
| Formula weight | 10205.105 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0ADZ0, Sequence view |
| ID 22 : 50S ribosomal protein L24 | |
| Image |   |
| Description | 50S ribosomal protein L24 |
| Type | polymer |
| Formula weight | 10823.674 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60624, Sequence view |
| ID 23 : 50S ribosomal protein L25 | |
| Image |   |
| Description | 50S ribosomal protein L25 |
| Type | polymer |
| Formula weight | 10713.566 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P68919, Sequence view |
| ID 24 : 50S ribosomal protein L27 | |
| Image |   |
| Description | 50S ribosomal protein L27 |
| Type | polymer |
| Formula weight | 9015.426 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7L8, Sequence view |
| ID 25 : 50S ribosomal protein L29 | |
| Image |   |
| Description | 50S ribosomal protein L29 |
| Type | polymer |
| Formula weight | 7087.321 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7M6, Sequence view |
| ID 26 : 50S ribosomal protein L30 | |
| Image |   |
| Description | 50S ribosomal protein L30 |
| Type | polymer |
| Formula weight | 6223.421 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG51, Sequence view |
| ID 27 : 50S ribosomal protein L32 | |
| Image |   |
| Description | 50S ribosomal protein L32 |
| Type | polymer |
| Formula weight | 3317.813 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7N4, Sequence view |
| ID 28 : 50S ribosomal protein L33 | |
| Image |   |
| Description | 50S ribosomal protein L33 |
| Type | polymer |
| Formula weight | 6015.169 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Genus: Escherichia NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7N9, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005878 |
| Name | 30S ribosomal protein L1 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:008932 |
| Name | 30S ribosomal protein L7/L12 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005880 |
| Name | 30S ribosomal protein L2 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000597 |
| Name | 30S ribosomal protein L3 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:013005 |
| Name | 30S ribosomal protein L4 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:002132 |
| Name | 30S ribosomal protein L5 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000702 |
| Name | 30S ribosomal protein L6 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000244 |
| Name | 30S ribosomal protein L9 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:006519 |
| Name | 30S ribosomal protein L11 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005823 |
| Name | 30S ribosomal protein L13 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005745 |
| Name | 30S ribosomal protein L14 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005749 |
| Name | 30S ribosomal protein L15 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000114 |
| Name | 30S ribosomal protein L16 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:000456 |
| Name | 30S ribosomal protein L17 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:004389 |
| Name | 30S ribosomal protein L18 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001857 |
| Name | 30S ribosomal protein L19 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005812 |
| Name | 30S ribosomal protein L20 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005727 |
| Name | 30S ribosomal protein L22 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001014 |
| Name | 30S ribosomal protein L23 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:003256 |
| Name | 30S ribosomal protein L24 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001021 |
| Name | 30S ribosomal protein L25 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001684 |
| Name | 30S ribosomal protein L27 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001854 |
| Name | 30S ribosomal protein L29 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:005996 |
| Name | 30S ribosomal protein L30 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:002677 |
| Name | 30S ribosomal protein L32 |
| Entity assembly | |
| Details | structural constituent of ribosome |
| GO-ID | GO:0003735 |
| InterPro-ID | IPR:001705 |
| Name | 30S ribosomal protein L33 |
| 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, spider |
| Target criteria | Minimization of number of poor van der Waals contacts and maximation of correlation coefficient |
| Refine hist | |
| Total atoms | 87129 |
| Nucleic acid atoms | 61134 |
| Protein atoms | 25995 |
 Download | |||
| PDB format | |||
| All | pdb2gya.ent.gzpdb2gya.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb2gya.ent.gz | ||
| mmCIF format | |||
| mmCIF | 2gya.cif.gz | ||
| XML format | |||
| All | 2gya.xml.gz | ||
| No-atom | 2gya-noatom.xml.gz | ||
| Ext-atom | 2gya-extatom.xml.gz | ||
| Movie files | |||
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| movie #4 |
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