Current Protein Identity：P62442
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 4V9J 70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state. Deposited 2013-04-23 | Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric（61） Consistent with all polymers |
Chain BK
2–141（140 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
2.9% PEG20000, 2.8% PPG P400, 5.1% PEG550 MME, 200 mM potassium thiocyanate, Tris acetate
|
Resolution 3.86 Å R-free 0.317 |
| 4V9J 70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state. Deposited 2013-04-23 | Assembly 2 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric（61） Consistent with all polymers |
Chain DK
2–141（140 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
2.9% PEG20000, 2.8% PPG P400, 5.1% PEG550 MME, 200 mM potassium thiocyanate, Tris acetate
|
Resolution 3.86 Å R-free 0.317 |
| 4V9K 70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state. Deposited 2013-04-24 | Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric（61） Consistent with all polymers |
Chain BK
2–141（140 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
2.9% PEG 20K, 2.8% PPG P400, 5.1% MME 550, KSCN 200 mM, TRIS ACETATE 100mM
|
Resolution 3.50 Å R-free 0.309 |
| 4V9K 70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state. Deposited 2013-04-24 | Assembly 2 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric（61） Consistent with all polymers |
Chain DK
2–141（140 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
2.9% PEG 20K, 2.8% PPG P400, 5.1% MME 550, KSCN 200 mM, TRIS ACETATE 100mM
|
Resolution 3.50 Å R-free 0.309 |
| 4V9L 70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC ACID/GDP, mRNA, and tRNA bound in the pe*/E state. Deposited 2013-04-24 | Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric（61） Consistent with all polymers |
Chain BK
2–141（140 aa）
|
Not recorded | FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
2.9% PEG 20K, 2.8% PPG P400, 5.1% MME 550, KSCN 200 mM, TRIS ACETATE 100mM
|
Resolution 3.50 Å R-free 0.328 |
| 4V9L 70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC ACID/GDP, mRNA, and tRNA bound in the pe*/E state. Deposited 2013-04-24 | Assembly 2 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric（61） Consistent with all polymers |
Chain DK
2–141（140 aa）
|
Not recorded | FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
2.9% PEG 20K, 2.8% PPG P400, 5.1% MME 550, KSCN 200 mM, TRIS ACETATE 100mM
|
Resolution 3.50 Å R-free 0.328 |
| 4V9M 70S Ribosome translocation intermediate FA-4.2A containing elongation factor EFG/FUSIDIC ACID/GDP, mRNA, and tRNA bound in the pe*/E state. Deposited 2013-04-25 | Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric（60） Consistent with all polymers |
Chain BK
2–141（140 aa）
|
Not recorded | FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
2.9% PEG 20K, 2.8% PPG P400, 5.1% MME 550, KSCN 200 mM, TRIS ACETATE 100mM
|
Resolution 4.00 Å R-free 0.329 |
| 4V9M 70S Ribosome translocation intermediate FA-4.2A containing elongation factor EFG/FUSIDIC ACID/GDP, mRNA, and tRNA bound in the pe*/E state. Deposited 2013-04-25 | Assembly 2 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric（60） Consistent with all polymers |
Chain DK
2–141（140 aa）
|
Not recorded | FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
2.9% PEG 20K, 2.8% PPG P400, 5.1% MME 550, KSCN 200 mM, TRIS ACETATE 100mM
|
Resolution 4.00 Å R-free 0.329 |
| 4V9N Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2. Deposited 2013-04-26 | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric（55） Consistent with all polymers |
Chain BK
1–147（147 aa）
|
Not recorded | MG MAGNESIUM ION × 1284 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7；pH 7.0
|
Resolution 3.40 Å R-free 0.268 |
| 4V9N Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2. Deposited 2013-04-26 | Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric（55） Consistent with all polymers |
Chain DK
1–147（147 aa）
|
Not recorded | MG MAGNESIUM ION × 1126 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7；pH 7.0
|
Resolution 3.40 Å R-free 0.268 |
| 4W29 70S ribosome translocation intermediate containing elongation factor EFG/GDP/fusidic acid, mRNA, and tRNAs trapped in the AP/AP pe/E chimeric hybrid state. Deposited 2014-07-02 | Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 61-meric（61） Consistent with all polymers |
Chain BK
2–141（140 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 FUA FUSIDIC ACID × 1 NMY NEOMYCIN × 4 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 3.80 Å R-free 0.331 |
| 4W29 70S ribosome translocation intermediate containing elongation factor EFG/GDP/fusidic acid, mRNA, and tRNAs trapped in the AP/AP pe/E chimeric hybrid state. Deposited 2014-07-02 | Assembly 2 Protein–RNA Heteromer；Protein × 55 PDB declaration: 61-meric（61） Consistent with all polymers |
Chain DK
2–141（140 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 FUA FUSIDIC ACID × 1 NMY NEOMYCIN × 2 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 3.80 Å R-free 0.331 |
| 4XEJ IRES bound to bacterial Ribosome Deposited 2014-12-23 | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric（53） Consistent with all polymers |
Chain AL11
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295.5 K；Initial crystallization screening was performed around conditions previously reported (31, 48) by dispensing 0.2 + 0.2 mL sitting drops with a Phoenix robotic liquid handling system (Art Robbins) on 96-well plates.
Once optimal crystallization conditions were determined, crystals were grown by the sitting-drop vapor-diffusion method using drops dispensed by the Phoenix with 1- to 2-mL ribosome complexes
mixed with 1-2 mL of reservoir solution [100 mM Tris-OAc, pH 7.0, 200 mM potassium thiocyanate (KSCN), 3.6-5% PEG 20,000, 6-14% 2-methyl-2,4-pentanediol (MPD)] at 22.5C.
Crystals emerged after 5-7 d and matured between 2-3 wk. Crystals were then subjected to cryoprotection by gradually replacing the mother liquor with cryoprotection buffer I
(100 mM Tris-OAc, pH 7.0, 200 mM KSCN, 5% PEG 20,000, 25% MPD, 14% PEG 200, and 10 mM Mg(OAc)2). The crystals then were flash-frozen by plunging into liquid nitrogen.
|
Resolution 3.80 Å R-free 0.284 |
| 4XEJ IRES bound to bacterial Ribosome Deposited 2014-12-23 | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric（53） Consistent with all polymers |
Chain BL11
1–147（147 aa）
|
Not recorded | ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295.5 K；Initial crystallization screening was performed around conditions previously reported (31, 48) by dispensing 0.2 + 0.2 mL sitting drops with a Phoenix robotic liquid handling system (Art Robbins) on 96-well plates.
Once optimal crystallization conditions were determined, crystals were grown by the sitting-drop vapor-diffusion method using drops dispensed by the Phoenix with 1- to 2-mL ribosome complexes
mixed with 1-2 mL of reservoir solution [100 mM Tris-OAc, pH 7.0, 200 mM potassium thiocyanate (KSCN), 3.6-5% PEG 20,000, 6-14% 2-methyl-2,4-pentanediol (MPD)] at 22.5C.
Crystals emerged after 5-7 d and matured between 2-3 wk. Crystals were then subjected to cryoprotection by gradually replacing the mother liquor with cryoprotection buffer I
(100 mM Tris-OAc, pH 7.0, 200 mM KSCN, 5% PEG 20,000, 25% MPD, 14% PEG 200, and 10 mM Mg(OAc)2). The crystals then were flash-frozen by plunging into liquid nitrogen.
|
Resolution 3.80 Å R-free 0.284 |
| 5A9Z Complex of Thermous thermophilus ribosome bound to BipA-GDPCP Deposited 2015-07-23 | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric（55） Consistent with all polymers |
Chain AJ
4–137（134 aa）
|
Not recorded | NMY NEOMYCIN × 2 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
5 MM HEPES PH 7.5, 10 MM MGAC, 50 MM KCL, 10 MM NH4CL, AND 6 MM 2- MERCAPTOETHANOL；pH 7.5；5 MM HEPES PH 7.5, 10 MM MGAC, 50 MM KCL, 10 MM NH4CL, AND 6 MM 2- MERCAPTOETHANOL
cryo-EM vitrification conditions
Cryogen ETHANE；LIQUID ETHANE
|
Resolution 4.70 Å |
| 5AA0 Complex of Thermous thermophilus ribosome (A-and P-site tRNA) bound to BipA-GDPCP Deposited 2015-07-23 | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric（58） Consistent with all polymers |
Chain AJ
4–137（134 aa）
|
Not recorded | NMY NEOMYCIN × 2 8AN 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) × 2 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
5 MM HEPES PH 7.5, 10 MM MGAC, 50 MM KCL, 10 MM NH4CL, AND 6 MM 2- MERCAPTOETHANOL；pH 7.5；5 MM HEPES PH 7.5, 10 MM MGAC, 50 MM KCL, 10 MM NH4CL, AND 6 MM 2- MERCAPTOETHANOL
cryo-EM vitrification conditions
Cryogen ETHANE；LIQUID ETHANE
|
Resolution 5.00 Å |
| 5D8B Crystal structure of T. thermophilus ribosome containing a P-site wobble mismatch Deposited 2015-08-17 | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 55-meric（55） Consistent with all polymers |
Chain G
1–147（147 aa）
|
Not recorded | MG MAGNESIUM ION × 1069 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；3.1 uL 70S*mRNA*tRNAfMet complex + 3.1 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate), reservoir: 300 uL 0.5-0.7 M sodium chloride, 3-fold molar excess of E. coli release factor 1 and 650 uM blasticidin S added during complex formation to stabilize the complex
|
Resolution 3.63 Å R-free 0.287 |
| 5D8B Crystal structure of T. thermophilus ribosome containing a P-site wobble mismatch Deposited 2015-08-17 | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 55-meric（55） Consistent with all polymers |
Chain CB
1–147（147 aa）
|
Not recorded | MG MAGNESIUM ION × 1149 ZN ZINC ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；3.1 uL 70S*mRNA*tRNAfMet complex + 3.1 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate), reservoir: 300 uL 0.5-0.7 M sodium chloride, 3-fold molar excess of E. coli release factor 1 and 650 uM blasticidin S added during complex formation to stabilize the complex
|
Resolution 3.63 Å R-free 0.287 |