3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
The Hsp15 protein fitted into the low resolution Cryo-EM map of the 50S.nc-tRNA.Hsp15 complex
by electron microscopy, at 10 A resolution
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3bbx |
|---|---|
| Title | The Hsp15 protein fitted into the low resolution Cryo-EM map of the 50S.nc-tRNA.Hsp15 complex |
| Descriptor | 50S ribosomal particle incomplete rRNA modeled |
| Keywords |  RIBOSOME, ribosomal complex, large subunit, 50S rescue stalled ribosome |
| Authors | Jiang, L., Abrahams, J.P. |
| Date | Deposition: 2007-11-11, Release: 2008-10-21 |
| 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-1455, Made by Jmol #3: With PDB-3bbu, PDB-3bbv, Made by Jmol #4: Superimposing with EM 3D map: EMDB-1455 (with PDB-3bbu, PDB-3bbv), 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 |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | J. Mol. Biol., Vol. 386, Issue 5, Page 1357-67, Year 2009 |
|---|---|
| Title | Recycling of aborted ribosomal 50S subunit-nascent chain-tRNA complexes by the heat shock protein Hsp15. |
| Authors | Linhua Jiang, Christiane Schaffitzel, Rouven Bingel-Erlenmeyer, Nenad Ban, Philipp Korber, Roman I Koning, Daniël C de Geus, Jasper R Plaisier, Jan Pieter Abrahams Department of Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands. |
| Keywords | Cryoelectron Microscopy, DNA-Binding Proteins (chemistry), Escherichia coli Proteins (chemistry), Heat-Shock Proteins (chemistry), Models, Molecular, Puromycin (chemistry, 53-79-2), RNA, Bacterial (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribosome Subunits, Large, Bacterial (chemistry), hslR protein, E coli |
| Links | PII: S0022-2836(08)01371-5, DOI: 10.1016/j.jmb.2008.10.079, PubMed: 19013177 |
 Components | |
| ID 1 : 5S ribosomal RNA | |
| Image |   |
|---|---|
| Description | 5S ribosomal RNA |
| Type | polymer |
| Formula weight | 38790.309 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli
Strain: MRE600 |
| Links | GenBank: 33357928, Sequence view |
| ID 2 : 23S ribosomal RNA | |
| Image |   |
| Description | 23S ribosomal RNA |
| Type | polymer |
| Formula weight | 941613.688 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | GenBank: 33357927, Sequence view |
| ID 3 : 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 NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P68919, Sequence view |
| ID 4 : 50S ribosomal protein L2 | |
| Image |   |
| Description | 50S ribosomal protein L2 |
| Type | polymer |
| Formula weight | 29923.838 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P60422, Sequence view |
| ID 5 : 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 NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P60438, Sequence view |
| ID 6 : 50S ribosomal protein L4 | |
| Image |   |
| Description | 50S ribosomal protein L4 |
| Type | polymer |
| Formula weight | 22121.723 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P60723, Sequence view |
| ID 7 : 50S ribosomal protein L5 | |
| Image |   |
| Description | 50S ribosomal protein L5 |
| Type | polymer |
| Formula weight | 20202.566 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P62399, Sequence view |
| ID 8 : 50S ribosomal protein L6 | |
| Image |   |
| Description | 50S ribosomal protein L6 |
| Type | polymer |
| Formula weight | 18801.766 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P02390, Sequence view |
| ID 9 : 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 NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7R1, Sequence view |
| ID 10 : 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 NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P02410, Sequence view |
| ID 11 : 50S ribosomal protein L14 | |
| Image |   |
| Description | 50S ribosomal protein L14 |
| Type | polymer |
| Formula weight | 13565.172 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P02411, Sequence view |
| ID 12 : 50S ribosomal protein L15 | |
| Image |   |
| Description | 50S ribosomal protein L15 |
| Type | polymer |
| Formula weight | 15008.598 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P02413, Sequence view |
| ID 13 : 50S ribosomal protein L16 | |
| Image |   |
| Description | 50S ribosomal protein L16 |
| Type | polymer |
| Formula weight | 15312.394 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P02414, Sequence view |
| ID 14 : 50S ribosomal protein L17 | |
| Image |   |
| Description | 50S ribosomal protein L17 |
| Type | polymer |
| Formula weight | 14393.774 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P02416, Sequence view |
| ID 15 : 50S ribosomal protein L18 | |
| Image |   |
| Description | 50S ribosomal protein L18 |
| Type | polymer |
| Formula weight | 12794.793 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0C018, Sequence view |
| ID 16 : 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 NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7K6, Sequence view |
| ID 17 : 50S ribosomal protein L20 | |
| Image |   |
| Description | 50S ribosomal protein L20 |
| Type | polymer |
| Formula weight | 13396.962 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7L3, Sequence view |
| ID 18 : 50S ribosomal protein L21 | |
| Image |   |
| Description | 50S ribosomal protein L21 |
| Type | polymer |
| Formula weight | 11586.485 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P02422, Sequence view |
| ID 19 : 50S ribosomal protein L22 | |
| Image |   |
| Description | 50S ribosomal protein L22 |
| Type | polymer |
| Formula weight | 12253.464 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P61175, Sequence view |
| ID 20 : 50S ribosomal protein L23 | |
| Image |   |
| Description | 50S ribosomal protein L23 |
| Type | polymer |
| Formula weight | 11222.270 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P02424, Sequence view |
| ID 21 : 50S ribosomal protein L24 | |
| Image |   |
| Description | 50S ribosomal protein L24 |
| Type | polymer |
| Formula weight | 11208.169 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P60624, Sequence view |
| ID 22 : 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 NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7L8, Sequence view |
| ID 23 : 50S ribosomal protein L29 | |
| Image |   |
| Description | 50S ribosomal protein L29 |
| Type | polymer |
| Formula weight | 7286.531 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7M6, Sequence view |
| ID 24 : 50S ribosomal protein L30 | |
| Image |   |
| Description | 50S ribosomal protein L30 |
| Type | polymer |
| Formula weight | 6423.682 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P02430, Sequence view |
| ID 25 : 50S ribosomal protein L31 | |
| Image |   |
| Description | 50S ribosomal protein L31 |
| Type | polymer |
| Formula weight | 7887.165 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7M9, Sequence view |
| ID 26 : 50S ribosomal protein L32 | |
| Image |   |
| Description | 50S ribosomal protein L32 |
| Type | polymer |
| Formula weight | 6332.307 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7N4, Sequence view |
| ID 27 : 50S ribosomal protein L33 | |
| Image |   |
| Description | 50S ribosomal protein L33 |
| Type | polymer |
| Formula weight | 6257.510 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7N9, Sequence view |
| ID 28 : 50S ribosomal protein L34 | |
| Image |   |
| Description | 50S ribosomal protein L34 |
| Type | polymer |
| Formula weight | 5397.506 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7P5, Sequence view |
| ID 29 : 50S ribosomal protein L35 | |
| Image |   |
| Description | 50S ribosomal protein L35 |
| Type | polymer |
| Formula weight | 7181.907 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7Q1, Sequence view |
| ID 30 : 50S ribosomal protein L36 | |
| Image |   |
| Description | 50S ribosomal protein L36 |
| Type | polymer |
| Formula weight | 4377.415 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:562Organism scientific: Escherichia coli Strain: MRE600 |
| Links | UniProt: P0A7Q6, Sequence view |
| ID 31 : MAGNESIUM ION | |
| Image |    |
| Description | MAGNESIUM ION |
| Type | non-polymer |
| Formula weight | 24.305 Da |
| Number of molecules | 110 |
| Source | Method: Obtained synthetically |
| ID 32 : water | |
| Image |   |
| Description | water |
| Type | water |
| Formula weight | 18.015 Da |
| Number of molecules | 506 |
| Source | Method: Isolated from a natural source |
 Sample |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: FEI Tecnai F20 |
|---|---|
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 200 kV |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | nominal: 50000 X |
| Cs | nominal: 2.0 mm |
| Nominal defocus | max: 3.5 nm, min: 1.5 nm |
| Detector | |
| Type | Kodak SO-163 film |
 Processing | |
| 2D projection selection | |
| Software name | situs, localfit |
|---|---|
| 3D reconstruction | |
| Actual pixel size | 2.54 A/pix |
| CTF correction method | CTF correction of each particle |
| Details | EMAN software |
| Method | cross-common lines, projection matching |
| Nominal pixel size | 2.54 A/pix |
| Resolution | 10 A |
| 3D fitting | |
| Method | colores |
| Refinement Protocol | multi-rigid body refinement |
| Refinement Space | RECIPROCAL |
| Software name | situs, localfit |
| Target criteria | best visual fit, best correlation value |
| Refine hist | |
| Solvent atoms | 506 |
| Total atoms | 89335 |
| Ligand atoms | 110 |
| Nucleic acid atoms | 63563 |
| Protein atoms | 25156 |
 Download | |||
| PDB format | |||
| All | pdb3bbx.ent.gzpdb3bbx.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb3bbx.ent.gz | ||
| mmCIF format | |||
| mmCIF | 3bbx.cif.gz | ||
| XML format | |||
| All | 3bbx.xml.gz | ||
| No-atom | 3bbx-noatom.xml.gz | ||
| Ext-atom | 3bbx-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-3bbx
Contact