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MODEL OF E. COLI SRP BOUND TO 70S RNCS
by single particle reconstruction, at 8 A resolution
#1: Depositted structure unit, Made by Jmol
#2: Superimposing with EM 3D map: EMDB-1261, Made by UCSF CHIMERA
#3: Superimposing with EM 3D map: EMDB-1262, Made by UCSF CHIMERA
#4: Superimposing with EM 3D map: EMDB-1263, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 2j28 |
|---|---|
| Title | MODEL OF E. COLI SRP BOUND TO 70S RNCS |
| Descriptor | 50S RIBOSOMAL PROTEIN L32 50S RIBOSOMAL PROTEIN L33 50S RIBOSOMAL PROTEIN L34 50S RIBOSOMAL PROTEIN L35 50S RIBOSOMAL PROTEIN L36 SIGNAL SEQUENCE SIGNAL RECOGNITION PARTICLE 54 50S RIBOSOMAL PROTEIN L2 50S RIBOSOMAL PROTEIN L4 50S RIBOSOMAL PROTEIN L5 50S RIBOSOMAL PROTEIN L6
50S RIBOSOMAL PROTEIN L9 50S RIBOSOMAL PROTEIN L11 50S RIBOSOMAL PROTEIN L13 50S RIBOSOMAL PROTEIN L14 50S RIBOSOMAL PROTEIN L15 50S RIBOSOMAL PROTEIN L16 50S RIBOSOMAL PROTEIN L17 50S RIBOSOMAL PROTEIN L18 50S RIBOSOMAL PROTEIN L19 50S RIBOSOMAL PROTEIN L20 50S RIBOSOMAL PROTEIN L21 50S RIBOSOMAL PROTEIN L22 50S RIBOSOMAL PROTEIN L23 50S RIBOSOMAL PROTEIN L24 50S RIBOSOMAL PROTEIN L25 50S RIBOSOMAL PROTEIN L27 50S RIBOSOMAL PROTEIN L29 50S RIBOSOMAL PROTEIN L30 50S RIBOSOMAL PROTEIN L31 |
| Keywords |  RIBOSOME, PROTEIN-RNA COMPLEX, SIGNAL RECOGNITION PARTICLE |
| 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 EM 3D map: EMDB-1261, Made by UCSF CHIMERA #3: Superimposing with EM 3D map: EMDB-1262, Made by UCSF CHIMERA #4: Superimposing with EM 3D map: EMDB-1263, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | Nature, Vol. 444, Page: 508 - 511, Year: 2006, |
|---|---|
| Title | Following the Signal Sequence from Ribosomal Tunnel Exit to Signal Recognition Particle |
| Authors | Halic, M., Blau, M., Becker, T., Mielke, T., Pool, M.R., Wild, K., Sinning, I., Beckmann, R. |
| Links | DOI: 10.1038/nature05326 |
 Components | |
| ID 1 : 50S RIBOSOMAL PROTEIN L32 | |
| Image |   |
|---|---|
| Description | 50S RIBOSOMAL PROTEIN L32 |
| Type | polypeptide(L) |
| Formula weight | 6332.307 Da |
| Number of molecules | 1 |
| ID | 1 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI
|
| Links | UniProt: P0A7N4, Sequence view |
| ID 2 : 50S RIBOSOMAL PROTEIN L33 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L33 |
| Type | polypeptide(L) |
| Formula weight | 6257.510 Da |
| Number of molecules | 1 |
| ID | 2 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7N9, Sequence view |
| ID 3 : 50S RIBOSOMAL PROTEIN L34 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L34 |
| Type | polypeptide(L) |
| Formula weight | 5397.506 Da |
| Number of molecules | 1 |
| ID | 3 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7P5, Sequence view |
| ID 4 : 50S RIBOSOMAL PROTEIN L35 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L35 |
| Type | polypeptide(L) |
| Formula weight | 7181.907 Da |
| Number of molecules | 1 |
| ID | 4 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7Q2, Sequence view |
| ID 5 : 50S RIBOSOMAL PROTEIN L36 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L36 |
| Type | polypeptide(L) |
| Formula weight | 4377.415 Da |
| Number of molecules | 1 |
| ID | 5 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7Q6, Sequence view |
| ID 6 : SIGNAL SEQUENCE | |
| Image |   |
| Description | SIGNAL SEQUENCE |
| Type | polypeptide(L) |
| Formula weight | 2121.567 Da |
| Number of molecules | 1 |
| ID | 6 |
| Source | Method: Obtained synthetically |
| Links | Sequence view |
| ID 7 : 4.5S SIGNAL RECOGNITION PARTICLE RNA | |
| Image |   |
| Description | 4.5S SIGNAL RECOGNITION PARTICLE RNA |
| Type | polyribonucleotide |
| Formula weight | 23968.469 Da |
| Number of molecules | 1 |
| ID | 7 |
| Source | Method: Obtained synthetically Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | Sequence view |
| ID 8 : SIGNAL RECOGNITION PARTICLE 54 | |
| Image |   |
| Description | SIGNAL RECOGNITION PARTICLE 54 |
| Type | polypeptide(L) |
| Formula weight | 47362.551 Da |
| Number of molecules | 1 |
| ID | 8 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0AGD7, Sequence view |
| ID 9 : 5S RIBOSOMAL RNA | |
| Image |   |
| Description | 5S RIBOSOMAL RNA |
| Type | polyribonucleotide |
| Formula weight | 37848.766 Da |
| Number of molecules | 1 |
| ID | 9 |
| Source | Method: Obtained synthetically Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | Sequence view |
| ID 10 : 23S RIBOSOMAL RNA | |
| Image |   |
| Description | 23S RIBOSOMAL RNA |
| Type | polyribonucleotide |
| Formula weight | 941613.688 Da |
| Number of molecules | 1 |
| ID | 10 |
| Source | Method: Obtained synthetically Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | Sequence view |
| ID 11 : 50S RIBOSOMAL PROTEIN L2 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L2 |
| Type | polypeptide(L) |
| Formula weight | 29248.984 Da |
| Number of molecules | 1 |
| ID | 11 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P60422, Sequence view |
| ID 12 : 50S RIBOSOMAL PROTEIN L3 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L3 |
| Type | polypeptide(L) |
| Formula weight | 22277.709 Da |
| Number of molecules | 1 |
| ID | 12 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P60438, Sequence view |
| ID 13 : 50S RIBOSOMAL PROTEIN L4 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L4 |
| Type | polypeptide(L) |
| Formula weight | 22121.723 Da |
| Number of molecules | 1 |
| ID | 13 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P60723, Sequence view |
| ID 14 : 50S RIBOSOMAL PROTEIN L5 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L5 |
| Type | polypeptide(L) |
| Formula weight | 20202.566 Da |
| Number of molecules | 1 |
| ID | 14 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P62399, Sequence view |
| ID 15 : 50S RIBOSOMAL PROTEIN L6 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L6 |
| Type | polypeptide(L) |
| Formula weight | 18801.766 Da |
| Number of molecules | 1 |
| ID | 15 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0AG55, Sequence view |
| ID 16 : 50S RIBOSOMAL PROTEIN L9 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L9 |
| Type | polypeptide(L) |
| Formula weight | 15789.174 Da |
| Number of molecules | 1 |
| ID | 16 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7R1, Sequence view |
| ID 17 : 50S RIBOSOMAL PROTEIN L11 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L11 |
| Type | polypeptide(L) |
| Formula weight | 14763.286 Da |
| Number of molecules | 1 |
| ID | 17 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7J7, Sequence view |
| ID 18 : 50S RIBOSOMAL PROTEIN L13 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L13 |
| Type | polypeptide(L) |
| Formula weight | 15822.503 Da |
| Number of molecules | 1 |
| ID | 18 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0AA10, Sequence view |
| ID 19 : 50S RIBOSOMAL PROTEIN L14 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L14 |
| Type | polypeptide(L) |
| Formula weight | 13320.821 Da |
| Number of molecules | 1 |
| ID | 19 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0ADY3, Sequence view |
| ID 20 : 50S RIBOSOMAL PROTEIN L15 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L15 |
| Type | polypeptide(L) |
| Formula weight | 15008.598 Da |
| Number of molecules | 1 |
| ID | 20 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P02413, Sequence view |
| ID 21 : 50S RIBOSOMAL PROTEIN L16 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L16 |
| Type | polypeptide(L) |
| Formula weight | 15312.394 Da |
| Number of molecules | 1 |
| ID | 21 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0ADY7, Sequence view |
| ID 22 : 50S RIBOSOMAL PROTEIN L17 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L17 |
| Type | polypeptide(L) |
| Formula weight | 14393.774 Da |
| Number of molecules | 1 |
| ID | 22 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0AG44, Sequence view |
| ID 23 : 50S RIBOSOMAL PROTEIN L18 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L18 |
| Type | polypeptide(L) |
| Formula weight | 12794.793 Da |
| Number of molecules | 1 |
| ID | 23 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0C018, Sequence view |
| ID 24 : 50S RIBOSOMAL PROTEIN L19 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L19 |
| Type | polypeptide(L) |
| Formula weight | 13028.207 Da |
| Number of molecules | 1 |
| ID | 24 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7K6, Sequence view |
| ID 25 : 50S RIBOSOMAL PROTEIN L20 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L20 |
| Type | polypeptide(L) |
| Formula weight | 13396.962 Da |
| Number of molecules | 1 |
| ID | 25 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7L3, Sequence view |
| ID 26 : 50S RIBOSOMAL PROTEIN L21 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L21 |
| Type | polypeptide(L) |
| Formula weight | 11586.485 Da |
| Number of molecules | 1 |
| ID | 26 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0AG48, Sequence view |
| ID 27 : 50S RIBOSOMAL PROTEIN L22 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L22 |
| Type | polypeptide(L) |
| Formula weight | 12253.464 Da |
| Number of molecules | 1 |
| ID | 27 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P61175, Sequence view |
| ID 28 : 50S RIBOSOMAL PROTEIN L23 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L23 |
| Type | polypeptide(L) |
| Formula weight | 11093.154 Da |
| Number of molecules | 1 |
| ID | 28 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0ADZ0, Sequence view |
| ID 29 : 50S RIBOSOMAL PROTEIN L24 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L24 |
| Type | polypeptide(L) |
| Formula weight | 11078.988 Da |
| Number of molecules | 1 |
| ID | 29 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P60624, Sequence view |
| ID 30 : 50S RIBOSOMAL PROTEIN L25 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L25 |
| Type | polypeptide(L) |
| Formula weight | 10713.566 Da |
| Number of molecules | 1 |
| ID | 30 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P68919, Sequence view |
| ID 31 : 50S RIBOSOMAL PROTEIN L27 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L27 |
| Type | polypeptide(L) |
| Formula weight | 9015.426 Da |
| Number of molecules | 1 |
| ID | 31 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7L8, Sequence view |
| ID 32 : 50S RIBOSOMAL PROTEIN L29 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L29 |
| Type | polypeptide(L) |
| Formula weight | 7286.531 Da |
| Number of molecules | 1 |
| ID | 32 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7M6, Sequence view |
| ID 33 : 50S RIBOSOMAL PROTEIN L30 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L30 |
| Type | polypeptide(L) |
| Formula weight | 6423.682 Da |
| Number of molecules | 1 |
| ID | 33 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0AG51, Sequence view |
| ID 34 : 50S RIBOSOMAL PROTEIN L31 | |
| Image |   |
| Description | 50S RIBOSOMAL PROTEIN L31 |
| Type | polypeptide(L) |
| Formula weight | 7887.165 Da |
| Number of molecules | 1 |
| ID | 34 |
| Source | Method: Isolated from a genetically manipulated source Gene: MRE600, ID:562, ESCHERICHIA COLIHost: ID:562, ESCHERICHIA COLI |
| Links | UniProt: P0A7M9, Sequence view |
| ID 35 : MAGNESIUM ION | |
| Image |    |
| Description | MAGNESIUM ION |
| Type | non-polymer |
| Formula weight | 24.305 Da |
| Number of molecules | 111 |
| ID | 35 |
| Source | Method: Obtained synthetically |
| ID 36 : water | |
| Image |   |
| Description | water |
| Type | water |
| Formula weight | 18.015 Da |
| Number of molecules | 512 |
| ID | 36 |
| Source | Method: Isolated from a natural source |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Name | SRP BOUND TO 70S RNCS |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample support | |
| Details | CARBON |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
 Electron Microscopy | |
| Imaging | |
| Microscope | Model: FEI TECNAI F30 |
|---|---|
| Electron gun | |
| Accelerating voltage | 300 kV |
| Lens | |
| Mode | BRIGHT FIELD |
 Processing | |
| 2D projection selection | |
| Software name | SPIDER |
|---|---|
| Single particle entity | |
| Symmetry type | ASYMMETRIC |
| Refine | |
| Refine id | ELECTRON MICROSCOPY |
| Ls d res high | 8.0 A |
| Refine hist | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| D res high | 8.0 |
| Solvent atoms | 512 |
| Total atoms | 95358 |
| Ligand atoms | 111 |
| Nucleic acid atoms | 65092 |
| Protein atoms | 29643 |
 Download | |||
| PDB format | |||
| All | pdb2j28.ent.gzpdb2j28.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb2j28.ent.gz | ||
| mmCIF format | |||
| mmCIF | 2j28.cif.gz | ||
| XML format | |||
| All | 2j28.xml.gz | ||
| No-atom | 2j28-noatom.xml.gz | ||
| Ext-atom | 2j28-extatom.xml.gz | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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| movie #3 |
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| movie #4 |
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