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Homology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome.
by single particle reconstruction, at 9.4 A resolution
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3bbn |
|---|---|
| Title | Homology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome. |
| Descriptor | small ribosomal subunit 30S |
| Keywords |  RIBOSOME, SMALL RIBOSOMAL SUBUNIT, SPINACH CHLOROPLAST RIBOSOME, RIBONUCLEOPROTEIN PARTICLE, MACROMOLECULAR COMPLEX |
| Authors | Sharma, M.R., Wilson, D.N., Datta, P.P., Barat, C., Schluenzen, F., Fucini, P., Agrawal, R.K. |
| Date | Deposition: 2007-11-09, Release: 2008-05-13 |
| 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-1417, Made by Jmol #3: With PDB-3bbo, Made by Jmol #5: Superimposing with EM 3D map: EMDB-1417 (with PDB-3bbo), 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 | Proc. Natl. Acad. Sci. U.S.A., Vol. 104, Issue 49, Page 19315-20, Year 2007 |
|---|---|
| Title | Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins. |
| Authors | Manjuli R Sharma, Daniel N Wilson, Partha P Datta, Chandana Barat, Frank Schluenzen, Paola Fucini, Rajendra K Agrawal Laboratory of Structural Pathology, Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA. |
| Keywords | Chloroplasts (chemistry), Cryoelectron Microscopy, Crystallography, X-Ray, Evolution, Molecular, Plant Proteins (chemistry), Plastids (chemistry), Protein Conformation, Ribosomal Proteins (chemistry), Ribosome Subunits, Large, Eukaryotic (chemistry), Ribosome Subunits, Small, Eukaryotic (chemistry), Spinacia oleracea (metabolism) |
| Links | DOI: 10.1073/pnas.0709856104, PubMed: 18042701, PMC: PMC2148287 |
 Components | |
| ID 1 : 16S rRNA | |
| Image |   |
|---|---|
| Description | 16S rRNA |
| Type | polymer |
| Formula weight | 483491.750 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | GenBank: 7636084, Sequence view |
| ID 2 : Ribosomal Protein S2 | |
| Image |   |
| Description | Ribosomal Protein S2 |
| Type | polymer |
| Formula weight | 26092.477 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P08242, Sequence view |
| ID 3 : Ribosomal Protein S3 | |
| Image |   |
| Description | Ribosomal Protein S3 |
| Type | polymer |
| Formula weight | 24965.348 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P09595, Sequence view |
| ID 4 : Ribosomal Protein S4 | |
| Image |   |
| Description | Ribosomal Protein S4 |
| Type | polymer |
| Formula weight | 23454.705 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P13788, Sequence view |
| ID 5 : Ribosomal Protein S5 | |
| Image |   |
| Description | Ribosomal Protein S5 |
| Type | polymer |
| Formula weight | 33626.633 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: Q9ST69, Sequence view |
| ID 6 : Ribosomal Protein S6 | |
| Image |   |
| Description | Ribosomal Protein S6 |
| Type | polymer |
| Formula weight | 18870.516 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P82403, Sequence view |
| ID 7 : Ribosomal Protein S7 | |
| Image |   |
| Description | Ribosomal Protein S7 |
| Type | polymer |
| Formula weight | 17378.459 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P82129, Sequence view |
| ID 8 : Ribosomal Protein S8 | |
| Image |   |
| Description | Ribosomal Protein S8 |
| Type | polymer |
| Formula weight | 15527.367 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P09597, Sequence view |
| ID 9 : Ribosomal Protein S9 | |
| Image |   |
| Description | Ribosomal Protein S9 |
| Type | polymer |
| Formula weight | 21351.033 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P82278, Sequence view |
| ID 10 : Ribosomal Protein S10 | |
| Image |   |
| Description | Ribosomal Protein S10 |
| Type | polymer |
| Formula weight | 21632.775 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | Sequence view |
| ID 11 : Ribosomal Protein S11 | |
| Image |   |
| Description | Ribosomal Protein S11 |
| Type | polymer |
| Formula weight | 15085.819 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P06506, Sequence view |
| ID 12 : Ribosomal Protein S12 | |
| Image |   |
| Description | Ribosomal Protein S12 |
| Type | polymer |
| Formula weight | 13794.378 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P62128, Sequence view |
| ID 13 : Ribosomal Protein S13 | |
| Image |   |
| Description | Ribosomal Protein S13 |
| Type | polymer |
| Formula weight | 16306.214 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P82163, Sequence view |
| ID 14 : Ribosomal Protein S14 | |
| Image |   |
| Description | Ribosomal Protein S14 |
| Type | polymer |
| Formula weight | 11809.930 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P06507, Sequence view |
| ID 15 : Ribosomal Protein S15 | |
| Image |   |
| Description | Ribosomal Protein S15 |
| Type | polymer |
| Formula weight | 10778.859 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: Q9M3I4, Sequence view |
| ID 16 : Ribosomal Protein S16 | |
| Image |   |
| Description | Ribosomal Protein S16 |
| Type | polymer |
| Formula weight | 10454.338 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P28807, Sequence view |
| ID 17 : Ribosomal Protein S17 | |
| Image |   |
| Description | Ribosomal Protein S17 |
| Type | polymer |
| Formula weight | 15828.815 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | Sequence view |
| ID 18 : Ribosomal Protein S18 | |
| Image |   |
| Description | Ribosomal Protein S18 |
| Type | polymer |
| Formula weight | 12337.539 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: Q9M3K7, Sequence view |
| ID 19 : Ribosomal Protein S19 | |
| Image |   |
| Description | Ribosomal Protein S19 |
| Type | polymer |
| Formula weight | 10632.598 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | UniProt: P06508, Sequence view |
| ID 20 : Ribosomal Protein S20 | |
| Image |   |
| Description | Ribosomal Protein S20 |
| Type | polymer |
| Formula weight | 21866.514 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | Sequence view |
| ID 21 : Ribosomal Protein S21 | |
| Image |   |
| Description | Ribosomal Protein S21 |
| Type | polymer |
| Formula weight | 21701.436 Da |
| Number of molecules | 1 |
| Details | modeled using Escherichia coli 2AVY as template |
| Source | Method: Isolated from a natural source Common name: spinach Cellular location: chloroplast NCBI taxonomy: ID:3562Organism scientific: Spinacea oleracea |
| Links | Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Details | tight couple chloroplast 70S ribosomes |
| Name | spinach 70S chloro-ribosome |
| Buffer | |
| Name | 10mM Tris-HCL pH 7.6, 50mM KCL, 10mM MgOAc, 7mM 2-ME |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 7.6 |
| Vitrification | |
| Details | 5 microliters applied to the grid then blotted for 3 seconds with Whatman number 1 filter paper before plunging in liquid ethane. |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: Phillips Tecnai F20 FEG |
|---|---|
| Electron gun | |
| Electron source | FEG |
| Accelerating voltage | 200 kV |
| Electron dose | 2000 e/A**2 |
| Illumination mode | Flood Beam |
| Lens | |
| Mode | Bright Field |
| Magnification | calibrated: 50760 X, nominal: 50000 X |
| Cs | nominal: 2 mm |
| Nominal defocus | max: 3500 nm, min: 700 nm |
| Specimen holder | |
| Tilt angle | min: 0 degrees, max: 0 degrees |
| Temperature | 93 Kelvin |
| Detector | |
| Type | Kodak S0163 Film |
 Processing | |
| Single particle entity | |
| Symmetry type | ASYMMETRIC |
|---|---|
| 3D reconstruction | |
| Actual pixel size | 2.76 A/pix |
| CTF correction method | CTF correction for each Micrograph |
| Details | An 11.5 A E.coli 70S ribosome map was used as initial reference and then resulting 18 A map from reconstruction of 70S chloro-ribosome was used as a reference for iterative refinement |
| Magnification calibration | 50,760 |
| Method | The projection matching procedure within the SPIDER software was used to get 3D map |
| Resolution | 9.4 A |
| 3D fitting | |
| Method | Cross-Correlation based manual fitting in 'O' |
| Refinement Protocol | Rigid Body |
| Refinement Space | REAL |
| Target criteria | Best visual fit using the program O |
| 3D fitting list | |
| PDB entry ID | 2XYZ and 2ZXY for small and large subunit respectively |
| Refine hist | |
| Total atoms | 51118 |
| Nucleic acid atoms | 31745 |
| Protein atoms | 19373 |
 Download | |||
| PDB format | |||
| All | pdb3bbn.ent.gzpdb3bbn.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb3bbn.ent.gz | ||
| mmCIF format | |||
| mmCIF | 3bbn.cif.gz | ||
| XML format | |||
| All | 3bbn.xml.gz | ||
| No-atom | 3bbn-noatom.xml.gz | ||
| Ext-atom | 3bbn-extatom.xml.gz | ||
| Movie files | |||
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