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Structure of the 50S subunit of E. coli ribosome in Pre-accommodation state
by electron microscopy, at 9 A resolution
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3e1b |
|---|---|
| Title | Structure of the 50S subunit of E. coli ribosome in Pre-accommodation state |
| Descriptor | Ribosome 50S subunit |
| Keywords |  RIBOSOME, ribosome, translation, accommodation, tRNA selection, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, Methylation, tRNA-binding, Phosphoprotein, Antibiotic resistance, Metal-binding, Repressor, Translation regulation |
| 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 |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Split: split data constructing the same model |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | To be Published, Vol. , Page: - , Year: , |
|---|---|
| Title | The Structure of the E. coli Ribosome Before and After Accommodation: Implications for Proofreading |
| Authors | Devkota, B., Caulfield, T.R., Tan, R.-Z., Harvey, S.C. |
 Components | |
| ID 1 : 5S rRNA | |
| Image |   |
|---|---|
| Description | 5S rRNA |
| Type | polyribonucleotide |
| Formula weight | 37848.766 Da |
| Number of molecules | 1 |
| ID | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli
|
| Links | GenBank: 170517292, Sequence view |
| ID 2 : 23S rRNA | |
| Image |   |
| Description | 23S rRNA |
| Type | polyribonucleotide |
| Formula weight | 941307.500 Da |
| Number of molecules | 1 |
| ID | 2 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | GenBank: 169887498, Sequence view |
| ID 3 : 50S ribosomal protein L25 | |
| Image |   |
| Description | 50S ribosomal protein L25 |
| Type | polypeptide(L) |
| Formula weight | 10713.566 Da |
| Number of molecules | 1 |
| ID | 3 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P68919, Sequence view |
| ID 4 : 50S ribosomal protein L14 | |
| Image |   |
| Description | 50S ribosomal protein L14 |
| Type | polypeptide(L) |
| Formula weight | 13565.172 Da |
| Number of molecules | 1 |
| ID | 4 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0ADY3, Sequence view |
| ID 5 : 50S ribosomal protein L15 | |
| Image |   |
| Description | 50S ribosomal protein L15 |
| Type | polypeptide(L) |
| Formula weight | 15008.598 Da |
| Number of molecules | 1 |
| ID | 5 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P02413, Sequence view |
| ID 6 : 50S ribosomal protein L16 | |
| Image |   |
| Description | 50S ribosomal protein L16 |
| Type | polypeptide(L) |
| Formula weight | 15312.394 Da |
| Number of molecules | 1 |
| ID | 6 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0ADY7, Sequence view |
| ID 7 : 50S ribosomal protein L17 | |
| Image |   |
| Description | 50S ribosomal protein L17 |
| Type | polypeptide(L) |
| Formula weight | 14393.774 Da |
| Number of molecules | 1 |
| ID | 7 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG44, Sequence view |
| ID 8 : 50S ribosomal protein L18 | |
| Image |   |
| Description | 50S ribosomal protein L18 |
| Type | polypeptide(L) |
| Formula weight | 12794.793 Da |
| Number of molecules | 1 |
| ID | 8 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0C018, Sequence view |
| ID 9 : 50S ribosomal protein L19 | |
| Image |   |
| Description | 50S ribosomal protein L19 |
| Type | polypeptide(L) |
| Formula weight | 13159.399 Da |
| Number of molecules | 1 |
| ID | 9 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7K6, Sequence view |
| ID 10 : 50S ribosomal protein L20 | |
| Image |   |
| Description | 50S ribosomal protein L20 |
| Type | polypeptide(L) |
| Formula weight | 13528.153 Da |
| Number of molecules | 1 |
| ID | 10 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7L3, Sequence view |
| ID 11 : 50S ribosomal protein L21 | |
| Image |   |
| Description | 50S ribosomal protein L21 |
| Type | polypeptide(L) |
| Formula weight | 11586.485 Da |
| Number of molecules | 1 |
| ID | 11 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG48, Sequence view |
| ID 12 : 50S ribosomal protein L22 | |
| Image |   |
| Description | 50S ribosomal protein L22 |
| Type | polypeptide(L) |
| Formula weight | 12253.464 Da |
| Number of molecules | 1 |
| ID | 12 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P61175, Sequence view |
| ID 13 : 50S ribosomal protein L23 | |
| Image |   |
| Description | 50S ribosomal protein L23 |
| Type | polypeptide(L) |
| Formula weight | 11093.154 Da |
| Number of molecules | 1 |
| ID | 13 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0ADZ0, Sequence view |
| ID 14 : 50S ribosomal protein L2 | |
| Image |   |
| Description | 50S ribosomal protein L2 |
| Type | polypeptide(L) |
| Formula weight | 29550.385 Da |
| Number of molecules | 1 |
| ID | 14 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60422, Sequence view |
| ID 15 : 50S ribosomal protein L24 | |
| Image |   |
| Description | 50S ribosomal protein L24 |
| Type | polypeptide(L) |
| Formula weight | 11210.181 Da |
| Number of molecules | 1 |
| ID | 15 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60624, Sequence view |
| ID 16 : 50S ribosomal protein L27 | |
| Image |   |
| Description | 50S ribosomal protein L27 |
| Type | polypeptide(L) |
| Formula weight | 9146.618 Da |
| Number of molecules | 1 |
| ID | 16 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7L8, Sequence view |
| ID 17 : 50S ribosomal protein L29 | |
| Image |   |
| Description | 50S ribosomal protein L29 |
| Type | polypeptide(L) |
| Formula weight | 7286.531 Da |
| Number of molecules | 1 |
| ID | 17 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7M6, Sequence view |
| ID 18 : 50S ribosomal protein L30 | |
| Image |   |
| Description | 50S ribosomal protein L30 |
| Type | polypeptide(L) |
| Formula weight | 6554.875 Da |
| Number of molecules | 1 |
| ID | 18 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG51, Sequence view |
| ID 19 : 50S ribosomal protein L31 | |
| Image |   |
| Description | 50S ribosomal protein L31 |
| Type | polypeptide(L) |
| Formula weight | 7887.165 Da |
| Number of molecules | 1 |
| ID | 19 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7M9, Sequence view |
| ID 20 : 50S ribosomal protein L32 | |
| Image |   |
| Description | 50S ribosomal protein L32 |
| Type | polypeptide(L) |
| Formula weight | 6463.500 Da |
| Number of molecules | 1 |
| ID | 20 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7N4, Sequence view |
| ID 21 : 50S ribosomal protein L33 | |
| Image |   |
| Description | 50S ribosomal protein L33 |
| Type | polypeptide(L) |
| Formula weight | 6257.510 Da |
| Number of molecules | 1 |
| ID | 21 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:624Organism scientific: Shigella sonnei |
| Links | UniProt: P0A7N9, Sequence view |
| ID 22 : 50S ribosomal protein L34 | |
| Image |   |
| Description | 50S ribosomal protein L34 |
| Type | polypeptide(L) |
| Formula weight | 5397.506 Da |
| Number of molecules | 1 |
| ID | 22 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:624Organism scientific: Shigella sonnei |
| Links | UniProt: P0A7P5, Sequence view |
| ID 23 : 50S ribosomal protein L35 | |
| Image |   |
| Description | 50S ribosomal protein L35 |
| Type | polypeptide(L) |
| Formula weight | 7181.907 Da |
| Number of molecules | 1 |
| ID | 23 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:624Organism scientific: Shigella sonnei |
| Links | UniProt: P0A7Q1, Sequence view |
| ID 24 : 50S ribosomal protein L36 | |
| Image |   |
| Description | 50S ribosomal protein L36 |
| Type | polypeptide(L) |
| Formula weight | 4377.415 Da |
| Number of molecules | 1 |
| ID | 24 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7Q6, Sequence view |
| ID 25 : 50S ribosomal protein L3 | |
| Image |   |
| Description | 50S ribosomal protein L3 |
| Type | polypeptide(L) |
| Formula weight | 22277.709 Da |
| Number of molecules | 1 |
| ID | 25 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60438, Sequence view |
| ID 26 : 50S ribosomal protein L1P | |
| Image |   |
| Description | 50S ribosomal protein L1P |
| Type | polypeptide(L) |
| Formula weight | 23978.254 Da |
| Number of molecules | 1 |
| ID | 26 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:2285Organism scientific: Sulfolobus acidocaldarius |
| Links | UniProt: P35024, Sequence view |
| ID 27 : 50S ribosomal protein L4 | |
| Image |   |
| Description | 50S ribosomal protein L4 |
| Type | polypeptide(L) |
| Formula weight | 22121.723 Da |
| Number of molecules | 1 |
| ID | 27 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P60723, Sequence view |
| ID 28 : 50S ribosomal protein L5 | |
| Image |   |
| Description | 50S ribosomal protein L5 |
| Type | polypeptide(L) |
| Formula weight | 20202.566 Da |
| Number of molecules | 1 |
| ID | 28 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P62399, Sequence view |
| ID 29 : 50S ribosomal protein L6 | |
| Image |   |
| Description | 50S ribosomal protein L6 |
| Type | polypeptide(L) |
| Formula weight | 18932.957 Da |
| Number of molecules | 1 |
| ID | 29 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AG55, Sequence view |
| ID 30 : 50S ribosomal protein L9 | |
| Image |   |
| Description | 50S ribosomal protein L9 |
| Type | polypeptide(L) |
| Formula weight | 15789.174 Da |
| Number of molecules | 1 |
| ID | 30 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7R1, Sequence view |
| ID 31 : 50S ribosomal protein L11 | |
| Image |   |
| Description | 50S ribosomal protein L11 |
| Type | polypeptide(L) |
| Formula weight | 14894.478 Da |
| Number of molecules | 1 |
| ID | 31 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0A7J7, Sequence view |
| ID 32 : 50S ribosomal protein L13 | |
| Image |   |
| Description | 50S ribosomal protein L13 |
| Type | polypeptide(L) |
| Formula weight | 15822.503 Da |
| Number of molecules | 1 |
| ID | 32 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli |
| Links | UniProt: P0AA10, Sequence view |
 Sample | |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
|---|---|
 Electron Microscopy |
 Processing | |
| 2D projection selection | |
| Software name | Yup.scx |
|---|---|
| 3D reconstruction | |
| Method | Single Particle |
| Nominal pixel size | 2.82 A/pix |
| Resolution | 9.0 A |
| 3D fitting | |
| Method | Flexible fitting |
| Refinement Space | REAL |
| Software name | Yup.scx |
| Target criteria | cross-correlation |
| 3D fitting list | |
| 3D fitting id | 1 |
| PDB entry ID | 2I2V |
| Refine hist | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| Total atoms | 92672 |
| Nucleic acid atoms | 64821 |
| Protein atoms | 27851 |
 Download | |||
| PDB format | |||
| All | pdb3e1b.ent.gzpdb3e1b.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb3e1b.ent.gz | ||
| mmCIF format | |||
| mmCIF | 3e1b.cif.gz | ||
| XML format | |||
| All | 3e1b.xml.gz | ||
| No-atom | 3e1b-noatom.xml.gz | ||
| Ext-atom | 3e1b-extatom.xml.gz | ||
| Movie files | |||
| movie #1 |
| ||
| movie #2 |
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