3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
T. thermophilus 70S ribosome in complex with mRNA, tRNAs and EF-Tu.GDP.kirromycin ternary complex, fitted to a 6.4 A Cryo-EM map. This file contains the 30S subunit and the ligands
by single particle reconstruction, at 6.4 A resolution
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3fic |
|---|---|
| Title | T. thermophilus 70S ribosome in complex with mRNA, tRNAs and EF-Tu.GDP.kirromycin ternary complex, fitted to a 6.4 A Cryo-EM map. This file contains the 30S subunit and the ligands |
| Descriptor | PROTEIN/RNA Complex |
| Keywords |  RIBOSOME, cryo-electron microscopy/elongation factor/GTPase/ribosome/translation, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, Metal-binding, Zinc-finger, tRNA-binding, Elongation factor, GTP-binding, Nucleotide-binding, Phosphoprotein, Protein biosynthesis |
| 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-5030, Made by Jmol #3: With PDB-3fin, Made by Jmol #5: Superimposing with EM 3D map: EMDB-5030 (with PDB-3fin), Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
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 | Embo J., Vol. 28, Page: 755 - 765, Year: 2009, |
|---|---|
| Title | GTPase activation of elongation factor EF-Tu by the ribosome during decoding |
| Authors | Schuette, J.C., Murphy, F.V., Kelley, A.C., Weir, J.R., Giesebrecht, J., Connell, S.R., Loerke, J., Mielke, T., Zhang, W., Penczek, P.A., Ramakrishnan, V., Spahn, C.M. |
| Links | DOI: 10.1038/emboj.2009.26 |
 Components | |
| ID 1 : 16S rRNA | |
| Image |   |
|---|---|
| Description | 16S rRNA |
| Type | polyribonucleotide |
| Formula weight | 488392.375 Da |
| Number of molecules | 1 |
| ID | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | Sequence view |
| ID 2 : 30S ribosomal protein S2 | |
| Image |   |
| Description | 30S ribosomal protein S2 |
| Type | polypeptide(L) |
| Formula weight | 27116.586 Da |
| Number of molecules | 1 |
| ID | 2 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: P80371, Sequence view |
| ID 3 : 30S ribosomal protein S4 | |
| Image |   |
| Description | 30S ribosomal protein S4 |
| Type | polypeptide(L) |
| Formula weight | 24242.426 Da |
| Number of molecules | 1 |
| ID | 3 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: P80373, Sequence view |
| ID 4 : 30S ribosomal protein S5 | |
| Image |   |
| Description | 30S ribosomal protein S5 |
| Type | polypeptide(L) |
| Formula weight | 16460.340 Da |
| Number of molecules | 1 |
| ID | 4 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SHQ5, Sequence view |
| ID 5 : 30S ribosomal protein S6 | |
| Image |   |
| Description | 30S ribosomal protein S6 |
| Type | polypeptide(L) |
| Formula weight | 11988.862 Da |
| Number of molecules | 1 |
| ID | 5 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SLP8, Sequence view |
| ID 6 : 30S ribosomal protein S8 | |
| Image |   |
| Description | 30S ribosomal protein S8 |
| Type | polypeptide(L) |
| Formula weight | 15868.703 Da |
| Number of molecules | 1 |
| ID | 6 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SHQ2, Sequence view |
| ID 7 : 30S ribosomal protein S11 | |
| Image |   |
| Description | 30S ribosomal protein S11 |
| Type | polypeptide(L) |
| Formula weight | 12606.479 Da |
| Number of molecules | 1 |
| ID | 7 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: P80376, Sequence view |
| ID 8 : 30S ribosomal protein S12 | |
| Image |   |
| Description | 30S ribosomal protein S12 |
| Type | polypeptide(L) |
| Formula weight | 13875.520 Da |
| Number of molecules | 1 |
| ID | 8 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SHN3, Sequence view |
| ID 9 : 30S ribosomal protein S15 | |
| Image |   |
| Description | 30S ribosomal protein S15 |
| Type | polypeptide(L) |
| Formula weight | 10447.311 Da |
| Number of molecules | 1 |
| ID | 9 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SJ76, Sequence view |
| ID 10 : 30S ribosomal protein S16 | |
| Image |   |
| Description | 30S ribosomal protein S16 |
| Type | polypeptide(L) |
| Formula weight | 9995.647 Da |
| Number of molecules | 1 |
| ID | 10 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SJH3, Sequence view |
| ID 11 : 30S ribosomal protein S17 | |
| Image |   |
| Description | 30S ribosomal protein S17 |
| Type | polypeptide(L) |
| Formula weight | 11880.210 Da |
| Number of molecules | 1 |
| ID | 11 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SHP7, Sequence view |
| ID 12 : 30S ribosomal protein S18 | |
| Image |   |
| Description | 30S ribosomal protein S18 |
| Type | polypeptide(L) |
| Formula weight | 8155.897 Da |
| Number of molecules | 1 |
| ID | 12 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SLQ0, Sequence view |
| ID 13 : 30S ribosomal protein S20 | |
| Image |   |
| Description | 30S ribosomal protein S20 |
| Type | polypeptide(L) |
| Formula weight | 10921.186 Da |
| Number of molecules | 1 |
| ID | 13 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: P80380, Sequence view |
| ID 14 : 30S ribosomal protein S3 | |
| Image |   |
| Description | 30S ribosomal protein S3 |
| Type | polypeptide(L) |
| Formula weight | 22975.789 Da |
| Number of molecules | 1 |
| ID | 14 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: P80372, Sequence view |
| ID 15 : 30S ribosomal protein S7 | |
| Image |   |
| Description | 30S ribosomal protein S7 |
| Type | polypeptide(L) |
| Formula weight | 17919.934 Da |
| Number of molecules | 1 |
| ID | 15 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: P17291, Sequence view |
| ID 16 : 30S ribosomal protein S9 | |
| Image |   |
| Description | 30S ribosomal protein S9 |
| Type | polypeptide(L) |
| Formula weight | 14298.604 Da |
| Number of molecules | 1 |
| ID | 16 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: P62669, Sequence view |
| ID 17 : 30S ribosomal protein S10 | |
| Image |   |
| Description | 30S ribosomal protein S10 |
| Type | polypeptide(L) |
| Formula weight | 11398.422 Da |
| Number of molecules | 1 |
| ID | 17 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SHN7, Sequence view |
| ID 18 : 30S ribosomal protein S13 | |
| Image |   |
| Description | 30S ribosomal protein S13 |
| Type | polypeptide(L) |
| Formula weight | 14207.793 Da |
| Number of molecules | 1 |
| ID | 18 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: P80377, Sequence view |
| ID 19 : 30S ribosomal protein S14 | |
| Image |   |
| Description | 30S ribosomal protein S14 |
| Type | polypeptide(L) |
| Formula weight | 7027.584 Da |
| Number of molecules | 1 |
| ID | 19 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SHQ1, Sequence view |
| ID 20 : 30S ribosomal protein S19 | |
| Image |   |
| Description | 30S ribosomal protein S19 |
| Type | polypeptide(L) |
| Formula weight | 9006.574 Da |
| Number of molecules | 1 |
| ID | 20 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SHP2, Sequence view |
| ID 21 : 30S ribosomal protein Thx | |
| Image |   |
| Description | 30S ribosomal protein Thx |
| Type | polypeptide(L) |
| Formula weight | 3089.684 Da |
| Number of molecules | 1 |
| ID | 21 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | UniProt: Q5SIH3, Sequence view |
| ID 22 : P-SITE TRNA | |
| Image |   |
| Description | P-SITE TRNA |
| Type | polyribonucleotide |
| Formula weight | 24816.971 Da |
| Number of molecules | 1 |
| ID | 22 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | Sequence view |
| ID 23 : SYNTHETIC MRNA | |
| Image |   |
| Description | SYNTHETIC MRNA |
| Type | polyribonucleotide |
| Formula weight | 1923.252 Da |
| Number of molecules | 1 |
| ID | 23 |
| Source | Method: Obtained synthetically |
| Links | Sequence view |
| ID 24 : E-SITE TRNA | |
| Image |   |
| Description | E-SITE TRNA |
| Type | polyribonucleotide |
| Formula weight | 24485.699 Da |
| Number of molecules | 1 |
| ID | 24 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | Sequence view |
| ID 25 : AT-SITE TRNA | |
| Image |   |
| Description | AT-SITE TRNA |
| Type | polyribonucleotide |
| Formula weight | 23583.510 Da |
| Number of molecules | 1 |
| ID | 25 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | Sequence view |
| ID 26 : MRNA CODON | |
| Image |   |
| Description | MRNA CODON |
| Type | polyribonucleotide |
| Formula weight | 873.547 Da |
| Number of molecules | 1 |
| ID | 26 |
| Source | Method: Obtained synthetically |
| Links | UniProt: Q5SHN6, Sequence view |
| ID 27 : Elongation factor Tu-A | |
| Image |   |
| Description | Elongation factor Tu-A |
| Type | polypeptide(L) |
| Formula weight | 44710.371 Da |
| Number of molecules | 1 |
| ID | 27 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:274Organism scientific: Thermus thermophilus |
| Links | Sequence view |
| ID 28 : PHENYLALANINAL | |
| Image |    |
| Description | PHENYLALANINAL |
| Type | non-polymer |
| Formula weight | 149.192 Da |
| Number of molecules | 1 |
| ID | 28 |
| Source | Method: Obtained synthetically |
| ID 29 : GUANOSINE-5'-DIPHOSPHATE | |
| Image |    |
| Description | GUANOSINE-5'-DIPHOSPHATE |
| Type | non-polymer |
| Formula weight | 443.203 Da |
| Number of molecules | 1 |
| ID | 29 |
| Source | Method: Obtained synthetically |
| ID 30 : N-METHYL KIRROMYCIN | |
| Image |    |
| Description | N-METHYL KIRROMYCIN |
| Type | non-polymer |
| Formula weight | 810.980 Da |
| Number of molecules | 1 |
| ID | 30 |
| Source | Method: Obtained synthetically |
| ID 31 : BETA-MERCAPTOETHANOL | |
| Image |    |
| Description | BETA-MERCAPTOETHANOL |
| Type | non-polymer |
| Formula weight | 78.129 Da |
| Number of molecules | 1 |
| ID | 31 |
| Source | Method: Obtained synthetically |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Details | 70S tRNA EF-Tu GDP kirromycin ribosomal complexes |
| Name | Thermus thermophilus ribosome complexed with mRNA, tRNAs and EF-Tu |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| Sample concentration | 30 mg/ml |
| Sample support | |
| Details | Quantifoil grids. |
| Vitrification | |
| Details | A Vitrobot was used to shock-freeze the sample in liquid methane. |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
 Electron Microscopy | |
| Imaging | |
| Microscope | Model: Tecnai Polara F30 |
|---|---|
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 300 kV |
| Electron dose | 2300 e/A**2 |
| Lens | |
| Mode | lowdose BRIGHT FIELD |
| Magnification | Nominal: 39000 X |
| Nominal defocus | Max: 4500 nm, Min: 1500 nm |
| Specimen holder | |
| Temperature | 77 Kelvin |
| Detector | |
| Type | Kodak SO-163 |
 Processing | |
| Single particle entity | |
| Symmetry type | ASYMMETRIC |
|---|---|
| 3D reconstruction | |
| Actual pixel size | 1.262 A/pix |
| CTF correction method | CTF correction of each defocus group volume prior to back projection. |
| Details | The SPIDER software package was used. |
| Method | projection matching |
| Nominal pixel size | 1.26 A/pix |
| Resolution | 6.4 A |
| 3D fitting | |
| Refinement Protocol | rigid body docking carried out with SPIDER or SITUS software. |
| Refinement Space | REAL |
| Target criteria | best visual fit using the programs O, CHIMERA or PYMOL. |
| Refine hist | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| Total atoms | 59525 |
| Ligand atoms | 101 |
| Nucleic acid atoms | 37335 |
| Protein atoms | 22089 |
 Download | |||
| PDB format | |||
| All | pdb3fic.ent.gzpdb3fic.ent (uncompressed file) | ||
|---|---|---|---|
| Header only | pdb3fic.ent.gz | ||
| mmCIF format | |||
| mmCIF | 3fic.cif.gz | ||
| XML format | |||
| All | 3fic.xml.gz | ||
| No-atom | 3fic-noatom.xml.gz | ||
| Ext-atom | 3fic-extatom.xml.gz | ||
| Movie files | |||
| movie #1 |
| ||
| movie #2 |
| ||
| movie #3 |
| ||
| movie #4 |
| ||
| movie #5 |
| ||
Top
Gallery
List
Diagram
Statistics
Documents
PDBj
EM Navigator
Detail page - PDB-3fic
Contact