50S ribosomal protein L11
OrganismNot specified
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein–RNA Heteromer Protein × 3 RNA 8 PDB declaration: undecameric（11） Consistent with all polymer counts | Chain G； UniProt 2–142 | Not recorded | ribosomal 23S RNA × 1 ribosomal 23S RNA × 1 ribosomal 23S RNA × 1 ribosomal 23S RNA × 1 ribosomal 23S RNA × 1 ribosomal 23S RNA × 1 ribosomal 16S RNA × 1 ribosomal 16S RNA × 1 30S ribosomal protein S12 × 1 （P0A7S3） Ribosome-recycling factor × 1 （Q9WX76） | ELECTRON MICROSCOPY cryo-EM buffer：BUFFER R；pH 7.5；BUFFER R cryo-EM vitrification conditions：Cryogen ETHANE；VITROBOT | Resolution 11.10 Å |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 3J0D | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2J28 MODEL OF E. COLI SRP BOUND TO 70S RNCS Deposited 2006-08-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric |
Chain I
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 111 |
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.50 Å |
| 2RDO 50S subunit with EF-G(GDPNP) and RRF bound Deposited 2007-09-24 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 34-meric |
Chain I
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
PolyMix；pH 7.5；PolyMix
cryo-EM vitrification conditions
Cryogen ETHANE；Rapid-freezing in liquid ethane by Vitrobot
|
Resolution 9.10 Å |
| 3DEG Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP Deposited 2008-06-10 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: undecameric |
Chain H
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
20 mM HEPES-KOH (pH 7.6), 4.5 mM Mg(CH3COO)2, 150 mM NH4CH3COO, 4 mM B-mercaptoethanol, 2 mM spermidine, and 0.05 mM spermine
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 10.90 Å |
| 3EP2 Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM Deposited 2008-09-29 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: nonameric |
Chain I
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.00 Å |
| 3EQ3 Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM Deposited 2008-09-30 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: nonameric |
Chain I
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；HiFi buffer (50 mM Tris-HCl pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 9.00 Å |
| 3EQ4 Model of tRNA(Leu)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM Deposited 2008-09-30 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: nonameric |
Chain I
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.3；Polymix buffer( 5 mM potassium phosphate (KH2PO4) pH 7.3, 5 mM NH4Cl, 95 mM KCl, 0.5 mM CaCl2, 8 mM putrescine, 1 mM spermidine, 1 mM DTE, 5 mM magnesium acetate)
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 12.00 Å |
| 3J5L Structure of the E. coli 50S subunit with ErmBL nascent chain Deposited 2013-10-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 34-meric |
Chain I
2–142（141 aa）
|
Not recorded | UNL UNKNOWN LIGAND × 1 ERY ERYTHROMYCIN A × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV)
|
Resolution 6.60 Å |
| 3J7Z Structure of the E. coli 50S subunit with ErmCL nascent chain Deposited 2014-08-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain I
1–142（142 aa）
|
Not recorded | ERY ERYTHROMYCIN A × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV).
|
Resolution 3.90 Å |
| 3J9Y Cryo-EM structure of tetracycline resistance protein TetM bound to a translating E.coli ribosome Deposited 2015-03-23 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM HEPES-KOH, 100 mM KOAc, 25 mM Mg(OAc)2, 6 mM b-mercaptoethanol；pH 7.4；50 mM HEPES-KOH, 100 mM KOAc, 25 mM Mg(OAc)2, 6 mM b-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV)
|
Resolution 3.90 Å |
| 3J9Z Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor G Deposited 2015-03-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain LE
2–142（141 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
93 K；Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV)
|
Resolution 3.60 Å |
| 3JA1 Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor G Deposited 2015-03-30 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain LK
2–142（141 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
93 K；Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV)
|
Resolution 3.60 Å |
| 3JBV Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps Deposited 2015-10-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain i
1–142（142 aa）
|
Not recorded | CLM CHLORAMPHENICOL × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
20mM HEPES, 50mM KOAc, 6mM Mg(OAc)2, 1mM DTT, 500 ug/ml chloramphenicol,0.05% Nikkol,0.5% pill/ml Complete EDTA-free Protease inhibitor cocktail,0.1 U/ml RNasin and 125mM sucrose；pH 7；20mM HEPES, 50mM KOAc, 6mM Mg(OAc)2, 1mM DTT, 500 ug/ml chloramphenicol,0.05% Nikkol,0.5% pill/ml Complete EDTA-free Protease inhibitor cocktail,0.1 U/ml RNasin and 125mM sucrose
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 3JCD Structure of Escherichia coli EF4 in posttranslocational ribosomes (Post EF4) Deposited 2015-12-01 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric |
Chain I
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 3JCE Structure of Escherichia coli EF4 in pretranslocational ribosomes (Pre EF4) Deposited 2015-12-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | PHE PHENYLALANINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 3JCJ Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association Deposited 2015-12-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain H
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 195 ZN ZINC ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
20 mM HEPES-KOH, pH 7.5, 15 mM magnesium acetate, 150 mM potassium acetate, 4 mM 2-mercapthoethanol, 2 mM spermidine, 0.05 mM spermine；pH 7.5；20 mM HEPES-KOH, pH 7.5, 15 mM magnesium acetate, 150 mM potassium acetate, 4 mM 2-mercapthoethanol, 2 mM spermidine, 0.05 mM spermine
cryo-EM vitrification conditions
Blot for 2-4 seconds before plunging；Cryogen ETHANE；Blot for 2-4 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).
|
Resolution 3.70 Å |
| 3JCN Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association: Initiation Complex I Deposited 2016-01-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric |
Chain I
1–142（142 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
20 mM HEPES-KOH, pH 7.5, 15 mM magnesium acetate, 150 mM potassium acetate, 4 mM 2-mercapthoethanol, 2 mM spermidine, 0.05 mM spermine；pH 7.5；20 mM HEPES-KOH, pH 7.5, 15 mM magnesium acetate, 150 mM potassium acetate, 4 mM 2-mercapthoethanol, 2 mM spermidine, 0.05 mM spermine
cryo-EM vitrification conditions
Blot for 2-4 seconds before plunging；Cryogen ETHANE；Blot for 2-4 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).
|
Resolution 4.60 Å |
| 4CSU Cryo-EM structures of the 50S ribosome subunit bound with ObgE Deposited 2014-03-10 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 33-meric |
Chain I
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
20MM TRIS-HCL, 100MM NH4CL,10MM MGCL2；pH 7.5；20MM TRIS-HCL, 100MM NH4CL,10MM MGCL2
cryo-EM vitrification conditions
Cryogen ETHANE；LIQUID ETHANE
|
Resolution 5.50 Å |
| 4U1U Crystal structure of the E. coli ribosome bound to quinupristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 271 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.95 Å R-free 0.282 |
| 4U1U Crystal structure of the E. coli ribosome bound to quinupristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 227 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.95 Å R-free 0.282 |
| 4U1V Crystal structure of the E. coli ribosome bound to linopristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 271 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 3.00 Å R-free 0.274 |
| 4U1V Crystal structure of the E. coli ribosome bound to linopristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 227 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 3.00 Å R-free 0.274 |
| 4U20 Crystal structure of the E. coli ribosome bound to flopristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 271 VIF Flopristin × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.90 Å R-free 0.279 |
| 4U20 Crystal structure of the E. coli ribosome bound to flopristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 227 VIF Flopristin × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.90 Å R-free 0.279 |
| 4U24 Crystal structure of the E. coli ribosome bound to dalfopristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 271 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.90 Å R-free 0.264 |
| 4U24 Crystal structure of the E. coli ribosome bound to dalfopristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 226 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.90 Å R-free 0.264 |
| 4U25 Crystal structure of the E. coli ribosome bound to virginiamycin M1. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 271 VIR VIRGINIAMYCIN M1 × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.90 Å R-free 0.265 |
| 4U25 Crystal structure of the E. coli ribosome bound to virginiamycin M1. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 227 VIR VIRGINIAMYCIN M1 × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.90 Å R-free 0.265 |
| 4U26 Crystal structure of the E. coli ribosome bound to dalfopristin and quinupristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 271 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.80 Å R-free 0.271 |
| 4U26 Crystal structure of the E. coli ribosome bound to dalfopristin and quinupristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 227 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.80 Å R-free 0.271 |
| 4U27 Crystal structure of the E. coli ribosome bound to flopristin and linopristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 271 VIF Flopristin × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.80 Å R-free 0.260 |
| 4U27 Crystal structure of the E. coli ribosome bound to flopristin and linopristin. Deposited 2014-07-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 227 VIF Flopristin × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.80 Å R-free 0.260 |
| 4V47 Real space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the EF-G.GTP state of E. coli 70S ribosome Deposited 2003-05-06 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 46-meric |
Chain AG
1–141（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
Tris；pH 7.5；Tris
cryo-EM vitrification conditions
Rapid-freezing in liquid ethane
|
Resolution 12.30 Å |
| 4V48 Real space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the initiation-like state of E. coli 70S ribosome Deposited 2003-05-06 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric |
Chain AG
1–141（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
hepes；pH 7.5；hepes
cryo-EM vitrification conditions
Rapid-freezing in liquid ethane
|
Resolution 11.50 Å |
| 4V4H Crystal structure of the bacterial ribosome from Escherichia coli in complex with the antibiotic kasugamyin at 3.5A resolution. Deposited 2006-08-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
1–142（142 aa）
|
Not recorded | KSG (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6-TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE × 1 MG MAGNESIUM ION × 170 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；MPD, PEG 8000, MGCL2, NH4CL, SPERMINE, SPERMIDINE, TRIS-HCL, EDTA, PH 7.5, BATCH, TEMPERATURE 277K, pH 7.50
|
Resolution 3.46 Å R-free 0.331 |
| 4V4H Crystal structure of the bacterial ribosome from Escherichia coli in complex with the antibiotic kasugamyin at 3.5A resolution. Deposited 2006-08-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
0–141（142 aa）
|
Not recorded | KSG (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6-TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE × 1 MG MAGNESIUM ION × 173 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；MPD, PEG 8000, MGCL2, NH4CL, SPERMINE, SPERMIDINE, TRIS-HCL, EDTA, PH 7.5, BATCH, TEMPERATURE 277K, pH 7.50
|
Resolution 3.46 Å R-free 0.331 |
| 4V4Q Crystal structure of the bacterial ribosome from Escherichia coli at 3.5 A resolution. Deposited 2005-08-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
1–141（141 aa）
|
Not recorded | MG MAGNESIUM ION × 170 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.46 Å R-free 0.331 |
| 4V4Q Crystal structure of the bacterial ribosome from Escherichia coli at 3.5 A resolution. Deposited 2005-08-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
1–141（141 aa）
|
Not recorded | MG MAGNESIUM ION × 173 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.46 Å R-free 0.331 |
| 4V4V Structure of a pre-translocational E. coli ribosome obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1056 Deposited 2006-05-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 52-meric |
Chain BG
2–140（139 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；rapid-freezing in liquid ethane
|
Resolution 15.00 Å |
| 4V4W Structure of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143 Deposited 2006-05-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 52-meric |
Chain BG
3–141（139 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；rapid-freezing in liquid ethane
|
Resolution 15.00 Å |
| 4V50 Crystal Structure of Ribosome with messenger RNA and the Anticodon stem-loop of P-site tRNA. Deposited 2006-08-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric |
Chain BI
1–141（141 aa）
|
Not recorded | MG MAGNESIUM ION × 181 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MGCL2, NH4CL, SPERMINE, SPERMIDINE, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.22 Å R-free 0.320 |
| 4V50 Crystal Structure of Ribosome with messenger RNA and the Anticodon stem-loop of P-site tRNA. Deposited 2006-08-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric |
Chain DI
1–141（141 aa）
|
Not recorded | MG MAGNESIUM ION × 177 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MGCL2, NH4CL, SPERMINE, SPERMIDINE, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.22 Å R-free 0.320 |
| 4V52 Crystal structure of the bacterial ribosome from Escherichia coli in complex with neomycin. Deposited 2007-06-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
2–142（141 aa）
|
Not recorded | NMY NEOMYCIN × 2 MG MAGNESIUM ION × 170 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.21 Å R-free 0.309 |
| 4V52 Crystal structure of the bacterial ribosome from Escherichia coli in complex with neomycin. Deposited 2007-06-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | NMY NEOMYCIN × 2 MG MAGNESIUM ION × 173 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.21 Å R-free 0.309 |
| 4V53 Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. Deposited 2007-06-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 170 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.54 Å R-free 0.320 |
| 4V53 Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. Deposited 2007-06-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 173 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.54 Å R-free 0.320 |
| 4V54 Crystal structure of the bacterial ribosome from Escherichia coli in complex with ribosome recycling factor (RRF). Deposited 2007-06-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 170 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.30 Å R-free 0.304 |
| 4V54 Crystal structure of the bacterial ribosome from Escherichia coli in complex with ribosome recycling factor (RRF). Deposited 2007-06-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 173 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.30 Å R-free 0.304 |
| 4V55 Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin and ribosome recycling factor (RRF). Deposited 2007-06-17 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 170 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 4.00 Å R-free 0.305 |
| 4V55 Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin and ribosome recycling factor (RRF). Deposited 2007-06-17 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 173 LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 4.00 Å R-free 0.305 |
| 4V56 Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin. Deposited 2007-07-21 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 170 SCM SPECTINOMYCIN × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.93 Å R-free 0.311 |
| 4V56 Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin. Deposited 2007-07-21 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 170 SCM SPECTINOMYCIN × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.93 Å R-free 0.311 |
| 4V57 Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin and neomycin. Deposited 2007-07-21 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
2–142（141 aa）
|
Not recorded | NMY NEOMYCIN × 2 MG MAGNESIUM ION × 170 SCM SPECTINOMYCIN × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.50 Å R-free 0.306 |
| 4V57 Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin and neomycin. Deposited 2007-07-21 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | NMY NEOMYCIN × 2 MG MAGNESIUM ION × 170 SCM SPECTINOMYCIN × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.50 Å R-free 0.306 |
| 4V5H E.Coli 70s Ribosome Stalled During Translation Of Tnac Leader Peptide. Deposited 2009-10-26 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain BI
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
50 MM TRIS-HCL PH 8.0, 10MM MG-ACETATE, 50MM KCL, 10MM NH4CL, 2MM EGTA, 2MM L-TRYPTOPHAN, 10 MM DTT；pH 8；50 MM TRIS-HCL PH 8.0, 10MM MG-ACETATE, 50MM KCL, 10MM NH4CL, 2MM EGTA, 2MM L-TRYPTOPHAN, 10 MM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；CRYOGEN- ETHANE,
|
Resolution 5.80 Å |
| 4V5Y Crystal structure of the bacterial ribosome from Escherichia coli in complex with paromomycin and ribosome recycling factor (RRF). Deposited 2007-06-19 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 170 PAR PAROMOMYCIN × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 4.45 Å R-free 0.309 |
| 4V5Y Crystal structure of the bacterial ribosome from Escherichia coli in complex with paromomycin and ribosome recycling factor (RRF). Deposited 2007-06-19 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 173 PAR PAROMOMYCIN × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 4.45 Å R-free 0.309 |
| 4V64 Crystal structure of the bacterial ribosome from Escherichia coli in complex with hygromycin B. Deposited 2008-06-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
1–141（141 aa）
|
Not recorded | MG MAGNESIUM ION × 170 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.50 Å R-free 0.318 |
| 4V64 Crystal structure of the bacterial ribosome from Escherichia coli in complex with hygromycin B. Deposited 2008-06-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
1–141（141 aa）
|
Not recorded | MG MAGNESIUM ION × 173 HYG HYGROMYCIN B × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 7.5；277 K；MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
|
Resolution 3.50 Å R-free 0.318 |
| 4V65 Structure of the E. coli ribosome in the Pre-accommodation state Deposited 2008-08-03 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric |
Chain B5
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.00 Å |
| 4V66 Structure of the E. coli ribosome and the tRNAs in Post-accommodation state Deposited 2008-08-03 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric |
Chain B5
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.00 Å |
| 4V69 Ternary complex-bound E.coli 70S ribosome. Deposited 2008-12-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain BI
2–142（141 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Vitrification using FEI Vitrobot; blot 3 seconds before plunging with an offset of -1mm
|
Resolution 6.70 Å |
| 4V6C Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting Deposited 2009-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 184 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；4% PEG 8000, 4% MPD, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, microbatch, temperature 291K
|
Resolution 3.19 Å R-free 0.252 |
| 4V6C Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting Deposited 2009-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 179 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；4% PEG 8000, 4% MPD, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, microbatch, temperature 291K
|
Resolution 3.19 Å R-free 0.252 |
| 4V6D Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting Deposited 2009-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric |
Chain BI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 184 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 7；291 K；4% PEG 8000, 4% MPD, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, pH 7.0, microbatch, temperature 291K
|
Resolution 3.81 Å R-free 0.253 |
| 4V6D Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting Deposited 2009-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric |
Chain DI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 179 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 7；291 K；4% PEG 8000, 4% MPD, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, pH 7.0, microbatch, temperature 291K
|
Resolution 3.81 Å R-free 0.253 |
| 4V6E Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting Deposited 2009-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 55-meric |
Chain BI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 184 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 7；291 K；4% PEG 8000, 4% MPD, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, pH 7.0, microbatch, temperature 291K
|
Resolution 3.71 Å R-free 0.268 |
| 4V6E Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting Deposited 2009-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 55-meric |
Chain DI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 179 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 7；291 K；4% PEG 8000, 4% MPD, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, pH 7.0, microbatch, temperature 291K
|
Resolution 3.71 Å R-free 0.268 |
| 4V6K Structural insights into cognate vs. near-cognate discrimination during decoding. Deposited 2011-01-07 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain AJ
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 8.25 Å |
| 4V6L Structural insights into cognate vs. near-cognate discrimination during decoding. Deposited 2011-01-07 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain BJ
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 13.20 Å |
| 4V6M Structure of the ribosome-SecYE complex in the membrane environment Deposited 2011-02-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 60-meric |
Chain BI
2–142（141 aa）
|
Not recorded | PEV (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 101 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol；pH 7.2；20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol
cryo-EM vitrification conditions
Cryogen ETHANE；liquid ethane was used as a cryogen
|
Resolution 7.10 Å |
| 4V6N Structural characterization of mRNA-tRNA translocation intermediates (50S ribosome of class2 of the six classes) Deposited 2011-12-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain AK
1–141（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 TRP TRYPTOPHAN × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)；pH 7.5；HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
cryo-EM vitrification conditions
blot for 3 seconds；80 K；Cryogen NITROGEN；Blot for 3 seconds, plunge into liquid nitrogen (Vitrobot)
|
Resolution 12.10 Å |
| 4V6O Structural characterization of mRNA-tRNA translocation intermediates (class 4a of the six classes) Deposited 2011-12-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain BK
1–141（141 aa）
|
Not recorded | TRP TRYPTOPHAN × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)；pH 7.5；HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
cryo-EM vitrification conditions
blot for 3 seconds；80 K；Cryogen NITROGEN；Blot for 3 seconds, plunge into liquid nitrogen (Vitrobot)
|
Resolution 14.70 Å |
| 4V6P Structural characterization of mRNA-tRNA translocation intermediates (class 4b of the six classes) Deposited 2011-12-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain BK
1–141（141 aa）
|
Not recorded | TRP TRYPTOPHAN × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)；pH 7.5；HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
cryo-EM vitrification conditions
blot for 6 seconds；80 K；Cryogen NITROGEN；Blot for 6 seconds, plunge into liquid nitrogen (Vitrobot)
|
Resolution 13.50 Å |
| 4V6Q Structural characterization of mRNA-tRNA translocation intermediates (class 5 of the six classes) Deposited 2011-12-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain BK
1–141（141 aa）
|
Not recorded | TRP TRYPTOPHAN × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)；pH 7.5；HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
cryo-EM vitrification conditions
blot for 3 seconds；80 K；Cryogen NITROGEN；Blot for 3 seconds, plunge into liquid nitrogen (Vitrobot)
|
Resolution 11.50 Å |
| 4V6R Structural characterization of mRNA-tRNA translocation intermediates (class 6 of the six classes) Deposited 2011-12-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain BK
1–141（141 aa）
|
Not recorded | TRP TRYPTOPHAN × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)；pH 7.5；HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
cryo-EM vitrification conditions
blot for 3 seconds；80 K；Cryogen NITROGEN；Blot for 3 seconds, plunge into liquid nitrogen (Vitrobot)
|
Resolution 11.50 Å |
| 4V6S Structural characterization of mRNA-tRNA translocation intermediates (class 3 of the six classes) Deposited 2011-12-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric |
Chain AK
1–141（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)；pH 7.5；HiFi buffer (50 mM Tris-HCl, pH 7.5, 70mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.5 mM spermidine, 8mM putrescine, 2 mM DTT, 3.5 mM MgCl2)
cryo-EM vitrification conditions
blot for 3 seconds；80 K；Cryogen NITROGEN；Blot for 3 seconds, plunge into liquid nitrogen (Vitrobot)
|
Resolution 13.10 Å |
| 4V6T Structure of the bacterial ribosome complexed by tmRNA-SmpB and EF-G during translocation and MLD-loading Deposited 2012-01-27 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain BI
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
blot for 5-10 seconds before plunging；96.15 K；Cryogen ETHANE；blot for 5-10 seconds before plunging into liquid ethane (FEI Vitrobot)
|
Resolution 8.30 Å |
| 4V6Y E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1a) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine；pH 7.5；50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Manual blotting for about 2 seconds；Cryogen ETHANE；Manual blotting for about 2 seconds prior to plunging into liquid ethane (custom-built CEVS vitrification instrument with dew point temperature adjusted to 18 degrees C)
|
Resolution 12.00 Å |
| 4V6Z E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1b) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 12.00 Å |
| 4V70 E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre3) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine；pH 7.5；50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Manual blotting for about 2 seconds；Cryogen ETHANE；Manual blotting for about 2 seconds prior to plunging into liquid ethane (custom-built CEVS vitrification instrument with dew point temperature adjusted to 18 degrees C)
|
Resolution 17.00 Å |
| 4V71 E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre2) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine；pH 7.5；50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Manual blotting for about 2 seconds；Cryogen ETHANE；Manual blotting for about 2 seconds prior to plunging into liquid ethane (custom-built CEVS vitrification instrument with dew point temperature adjusted to 18 degrees C)
|
Resolution 20.00 Å |
| 4V72 E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre4) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine；pH 7.5；50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Manual blotting for about 2 seconds；Cryogen ETHANE；Manual blotting for about 2 seconds prior to plunging into liquid ethane (custom-built CEVS vitrification instrument with dew point temperature adjusted to 18 degrees C)
|
Resolution 13.00 Å |
| 4V73 E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5a) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 15.00 Å |
| 4V74 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5b) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine；pH 7.5；50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Manual blotting for about 2 seconds；Cryogen ETHANE；Manual blotting for about 2 seconds prior to plunging into liquid ethane (custom-built CEVS vitrification instrument with dew point temperature adjusted to 18 degrees C)
|
Resolution 17.00 Å |
| 4V75 E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic post-translocation state (post1) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine；pH 7.5；50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Manual blotting for about 2 seconds；Cryogen ETHANE；Manual blotting for about 2 seconds prior to plunging into liquid ethane (custom-built CEVS vitrification instrument with dew point temperature adjusted to 18 degrees C)
|
Resolution 12.00 Å |
| 4V76 E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2a) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine；pH 7.5；50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Manual blotting for about 2 seconds；Cryogen ETHANE；Manual blotting for about 2 seconds prior to plunging into liquid ethane (custom-built CEVS vitrification instrument with dew point temperature adjusted to 18 degrees C)
|
Resolution 17.00 Å |
| 4V77 E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2b) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 17.00 Å |
| 4V78 E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3a) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 20.00 Å |
| 4V79 E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3b) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine；pH 7.5；50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Manual blotting for about 2 seconds；Cryogen ETHANE；Manual blotting for about 2 seconds prior to plunging into liquid ethane (custom-built CEVS vitrification instrument with dew point temperature adjusted to 18 degrees C)
|
Resolution 15.00 Å |
| 4V7A E. coli 70S-fMetVal-tRNAVal post-translocation complex (post4) Deposited 2013-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric |
Chain BI
1–142（142 aa）
|
Not recorded | VAL VALINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine；pH 7.5；50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Manual blotting for about 2 seconds；Cryogen ETHANE；Manual blotting for about 2 seconds prior to plunging into liquid ethane (custom-built CEVS vitrification instrument with dew point temperature adjusted to 18 degrees C)
|
Resolution 9.00 Å |
| 4V7B Visualization of two tRNAs trapped in transit during EF-G-mediated translocation Deposited 2013-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain BI
1–142（142 aa）
|
Not recorded | FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
80 mM HEPES potassium, 75 mM NH4Cl, 10 mM MgCl2, 6 mM BME；pH 7.6；80 mM HEPES potassium, 75 mM NH4Cl, 10 mM MgCl2, 6 mM BME
cryo-EM vitrification conditions
blot for 5-10 seconds before plunging；96 K；Cryogen ETHANE；Blot for 5-10 seconds before plunging into liquid ethane (FEI VITROBOT MARK I)
|
Resolution 6.80 Å |
| 4V7C Structure of the Ribosome with Elongation Factor G Trapped in the Pre-Translocation State (pre-translocation 70S*tRNA structure) Deposited 2013-11-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain BK
2–142（141 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
Polymix buffer；pH 7.6；10 mM HEPES-KOH, 5 mM MgCl2, 90 mM NH4Cl, 2 mM spermidine, 0.1 mM spermine, 6 mM BME, 0.5 mM viomycin, 0.5 mM GTP, 0.5 mM fusidic acid
cryo-EM vitrification conditions
Freshly glow-disharged grids were loaded into an FEI Mark II Vitrobot and equilibrated to 95% relative humidity at 22 degrees Celsius. 2 microliters of sample was applied through the side port, blotted for 7 seconds with a positional offset of 2, and plunged into liquid ethane.；Cryogen ETHANE；Freshly glow-disharged grids were loaded into an FEI Mark II Vitrobot and equilibrated to 95% relative humidity at 22 degrees Celsius. 2 microliters of sample was applied through the side port, blotted for 7 seconds with a positional offset of 2, and plunged into liquid ethane.
|
Resolution 7.60 Å |
| 4V7D Structure of the Ribosome with Elongation Factor G Trapped in the Pre-Translocation State (pre-translocation 70S*tRNA*EF-G structure) Deposited 2013-11-21 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 60-meric |
Chain AK
2–142（141 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
Polymix buffer；pH 7.6；10 mM HEPES-KOH, 5 mM MgCl2, 90 mM NH4Cl, 2 mM spermidine, 0.1 mM spermine, 6 mM BME, 0.5 mM viomycin, 0.5 mM GTP, 0.5 mM fusidic acid
cryo-EM vitrification conditions
Freshly glow-disharged grids were loaded into an FEI Mark II Vitrobot and equilibrated to 95% relative humidity at 22 degrees Celsius. 2 microliters of sample was applied through the side port, blotted for 7 seconds with a positional offset of 2, and plunged into liquid ethane.；Cryogen ETHANE；Freshly glow-disharged grids were loaded into an FEI Mark II Vitrobot and equilibrated to 95% relative humidity at 22 degrees Celsius. 2 microliters of sample was applied through the side port, blotted for 7 seconds with a positional offset of 2, and plunged into liquid ethane.
|
Resolution 7.60 Å |
| 4V7I Ribosome-SecY complex. Deposited 2009-10-21 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric |
Chain AI
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
50 MM HEPES- KOH PH 7.5, 100 MM KOAC, 10 MM MG(OAC)2, 0.05% DDM；pH 7.5；50 MM HEPES- KOH PH 7.5, 100 MM KOAC, 10 MM MG(OAC)2, 0.05% DDM
cryo-EM vitrification conditions
Cryogen ETHANE；THE SPECIMENS WERE PLUNGE FROZEN IN LIQUID ETHANE AT 4 DEGREES C AT AN RH OF ~90-95%.
|
Resolution 9.60 Å |
| 4V7S Crystal structure of the E. coli ribosome bound to telithromycin. Deposited 2010-08-05 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 181 TEL TELITHROMYCIN × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, pH 6.5, microbatch, temperature 291K
|
Resolution 3.25 Å R-free 0.245 |
| 4V7S Crystal structure of the E. coli ribosome bound to telithromycin. Deposited 2010-08-05 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 179 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, pH 6.5, microbatch, temperature 291K
|
Resolution 3.25 Å R-free 0.245 |
| 4V7T Crystal structure of the E. coli ribosome bound to chloramphenicol. Deposited 2010-08-14 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 183 CLM CHLORAMPHENICOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, pH 6.5, microbatch, temperature 291K
|
Resolution 3.19 Å R-free 0.252 |
| 4V7T Crystal structure of the E. coli ribosome bound to chloramphenicol. Deposited 2010-08-14 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 179 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, pH 6.5, microbatch, temperature 291K
|
Resolution 3.19 Å R-free 0.252 |
| 4V7U Crystal structure of the E. coli ribosome bound to erythromycin. Deposited 2010-08-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 182 ERY ERYTHROMYCIN A × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；4.3% PEG 8000, 4.9% MPD, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, 10 mM Tris, 20 mM MES pH 6.5. 0.25 mM EDTA, microbatch, temperature 291K
|
Resolution 3.10 Å R-free 0.254 |
| 4V7U Crystal structure of the E. coli ribosome bound to erythromycin. Deposited 2010-08-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 179 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；4.3% PEG 8000, 4.9% MPD, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, 10 mM Tris, 20 mM MES pH 6.5. 0.25 mM EDTA, microbatch, temperature 291K
|
Resolution 3.10 Å R-free 0.254 |
| 4V7V Crystal structure of the E. coli ribosome bound to clindamycin. Deposited 2010-08-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 182 CLY CLINDAMYCIN × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；4.3% PEG 8000, 4.9% MPD, 10 mM Tris, 20 mM MES, pH 6.5-7.0, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, 0.25 mM EDTA, microbatch, temperature 291K
|
Resolution 3.29 Å R-free 0.241 |
| 4V7V Crystal structure of the E. coli ribosome bound to clindamycin. Deposited 2010-08-16 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 179 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；4.3% PEG 8000, 4.9% MPD, 10 mM Tris, 20 mM MES, pH 6.5-7.0, 3.8 mM MgCl2, 380 mM NH4Cl, 5.5 mM putrescine, 5 mM spermidine, 0.25 mM EDTA, microbatch, temperature 291K
|
Resolution 3.29 Å R-free 0.241 |
| 4V89 Crystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome (without viomycin) Deposited 2011-11-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric |
Chain BI
1–142（142 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；Tris Ac PH.7.0 25-35 mM KCL 6.1% PEG 20000 %1 glycerol 50mM sucrose
, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 3.70 Å R-free 0.290 |
| 4V9C Allosteric control of the ribosome by small-molecule antibiotics Deposited 2012-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric |
Chain BI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 224 NMY NEOMYCIN × 10 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；291 K；PEG800, MPD, pH 6.5, microbatch, temperature 291K
|
Resolution 3.30 Å R-free 0.255 |
| 4V9C Allosteric control of the ribosome by small-molecule antibiotics Deposited 2012-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric |
Chain DI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 266 NMY NEOMYCIN × 8 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；291 K；PEG800, MPD, pH 6.5, microbatch, temperature 291K
|
Resolution 3.30 Å R-free 0.255 |
| 4V9D Structures of the bacterial ribosome in classical and hybrid states of tRNA binding Deposited 2012-07-31 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric |
Chain CI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 271 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
|
Resolution 3.00 Å R-free 0.260 |
| 4V9D Structures of the bacterial ribosome in classical and hybrid states of tRNA binding Deposited 2012-07-31 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 227 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
|
Resolution 3.00 Å R-free 0.260 |
| 4V9O Control of ribosomal subunit rotation by elongation factor G Deposited 2013-05-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric |
Chain AI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 187 ZN ZINC ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
|
Resolution 2.90 Å R-free 0.272 |
| 4V9O Control of ribosomal subunit rotation by elongation factor G Deposited 2013-05-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric |
Chain CI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 187 ZN ZINC ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
|
Resolution 2.90 Å R-free 0.272 |
| 4V9O Control of ribosomal subunit rotation by elongation factor G Deposited 2013-05-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric |
Chain EI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 187 ZN ZINC ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
|
Resolution 2.90 Å R-free 0.272 |
| 4V9O Control of ribosomal subunit rotation by elongation factor G Deposited 2013-05-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric |
Chain GI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 187 ZN ZINC ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
|
Resolution 2.90 Å R-free 0.272 |
| 4V9P Control of ribosomal subunit rotation by elongation factor G Deposited 2013-05-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric |
Chain AI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 185 ZN ZINC ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
|
Resolution 2.90 Å R-free 0.267 |
| 4V9P Control of ribosomal subunit rotation by elongation factor G Deposited 2013-05-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric |
Chain CI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 185 ZN ZINC ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
|
Resolution 2.90 Å R-free 0.267 |
| 4V9P Control of ribosomal subunit rotation by elongation factor G Deposited 2013-05-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric |
Chain EI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 185 ZN ZINC ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
|
Resolution 2.90 Å R-free 0.267 |
| 4V9P Control of ribosomal subunit rotation by elongation factor G Deposited 2013-05-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain GI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 185 ZN ZINC ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, KSCN, pH 6.5, microbatch, temperature 291K
|
Resolution 2.90 Å R-free 0.267 |
| 4WF1 Crystal structure of the E. coli ribosome bound to negamycin. Deposited 2014-09-11 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain BI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 271 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 3.09 Å R-free 0.244 |
| 4WF1 Crystal structure of the E. coli ribosome bound to negamycin. Deposited 2014-09-11 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain DI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 228 ZN ZINC ION × 1 NEG NEGAMYCIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 3.09 Å R-free 0.244 |
| 4WOI 4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2 Deposited 2014-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 269 PAR PAROMOMYCIN × 6 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KCl, KSCN
|
Resolution 3.00 Å R-free 0.253 |
| 4WOI 4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2 Deposited 2014-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric |
Chain CI
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 226 PAR PAROMOMYCIN × 7 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KCl, KSCN
|
Resolution 3.00 Å R-free 0.253 |
| 4WWW Crystal structure of the E. coli ribosome bound to CEM-101 Deposited 2014-11-12 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain RI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 182 EM1 (3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 3.10 Å R-free 0.252 |
| 4WWW Crystal structure of the E. coli ribosome bound to CEM-101 Deposited 2014-11-12 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain YI
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 179 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 3.10 Å R-free 0.252 |
| 4YBB High-resolution structure of the Escherichia coli ribosome Deposited 2015-02-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 263 PG4 TETRAETHYLENE GLYCOL × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 14 PUT 1,4-DIAMINOBUTANE × 16 ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 11 SPD SPERMIDINE × 4 1PE PENTAETHYLENE GLYCOL × 2 PGE TRIETHYLENE GLYCOL × 9 ACY ACETIC ACID × 3 EDO 1,2-ETHANEDIOL × 12 GUN GUANINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.10 Å R-free 0.234 |
| 4YBB High-resolution structure of the Escherichia coli ribosome Deposited 2015-02-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain CJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 200 PG4 TETRAETHYLENE GLYCOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 2.10 Å R-free 0.234 |
| 5ADY Cryo-EM structures of the 50S ribosome subunit bound with HflX Deposited 2015-08-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 34-meric |
Chain I
1–142（142 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
20MM TRIS-HCL, 100MM NH4CL, 10MM MGCL2；pH 7.5；20MM TRIS-HCL, 100MM NH4CL, 10MM MGCL2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 5AFI 2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM Deposited 2015-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 333 CL CHLORIDE ION × 2 FME N-FORMYLMETHIONINE × 1 KIR KIRROMYCIN × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 NA SODIUM ION × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
50MM HEPES-KOH, 70MMNH4CL, 30MM KCL, 20MM MGCL2, 1MM DTT, 0.6MM SPERMINE, 0.4MM SPERMIDINE, 0.15MM KIRROMYCIN；pH 7.5；50MM HEPES-KOH, 70MMNH4CL, 30MM KCL, 20MM MGCL2, 1MM DTT, 0.6MM SPERMINE, 0.4MM SPERMIDINE, 0.15MM KIRROMYCIN
cryo-EM vitrification conditions
Cryogen ETHANE；LIQUIDE ETHANE
|
Resolution 2.90 Å |
| 5AKA EM structure of ribosome-SRP-FtsY complex in closed state Deposited 2015-03-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 34-meric |
Chain I
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 110 |
ELECTRON MICROSCOPY
cryo-EM buffer
50MM HEPES-KOH, 100MM KOAC, 8MM MG(OAC)2, 500UG/ML CHLORAMPHENICO；pH 7.5；50MM HEPES-KOH, 100MM KOAC, 8MM MG(OAC)2, 500UG/ML CHLORAMPHENICO
cryo-EM vitrification conditions
Cryogen ETHANE；LIQUID ETHAN
|
Resolution 5.70 Å |
| 5GAD RNC-SRP-SR complex early state Deposited 2015-11-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 37-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 433 ZN ZINC ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 5GAE RNC in complex with a translocating SecYEG Deposited 2015-11-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 36-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 323 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 5GAF RNC in complex with SRP Deposited 2015-11-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 36-meric |
Chain J
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 431 ZN ZINC ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 5GAG RNC in complex with SRP-SR in the closed state Deposited 2015-11-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 36-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 431 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 5GAH RNC in complex with SRP with detached NG domain Deposited 2015-11-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 36-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 431 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 5H5U Mechanistic insights into the alternative translation termination by ArfA and RF2 Deposited 2016-11-09 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric |
Chain J
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 5IQR Structure of RelA bound to the 70S ribosome Deposited 2016-03-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 299 ZN ZINC ION × 3 PAR PAROMOMYCIN × 1 MET METHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Grids were blotted for 5 s
|
Resolution 3.00 Å |
| 5IT8 High-resolution structure of the Escherichia coli ribosome Deposited 2016-03-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 266 PG4 TETRAETHYLENE GLYCOL × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 14 PUT 1,4-DIAMINOBUTANE × 16 ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 11 EDO 1,2-ETHANEDIOL × 12 PGE TRIETHYLENE GLYCOL × 9 SPD SPERMIDINE × 4 1PE PENTAETHYLENE GLYCOL × 2 ACY ACETIC ACID × 3 GUN GUANINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 3.12 Å R-free 0.220 |
| 5IT8 High-resolution structure of the Escherichia coli ribosome Deposited 2016-03-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain CJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 200 PG4 TETRAETHYLENE GLYCOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD
|
Resolution 3.12 Å R-free 0.220 |
| 5J5B Structure of the WT E coli ribosome bound to tetracycline Deposited 2016-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 267 PG4 TETRAETHYLENE GLYCOL × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 14 PUT 1,4-DIAMINOBUTANE × 16 TAC TETRACYCLINE × 1 ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 11 EDO 1,2-ETHANEDIOL × 12 PGE TRIETHYLENE GLYCOL × 9 SPD SPERMIDINE × 4 1PE PENTAETHYLENE GLYCOL × 2 ACY ACETIC ACID × 3 GUN GUANINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；PEG 8000, Spermidine, Putrescine, Ammonium Chloride, Magnesium Chloride, MES pH 6.5
|
Resolution 2.80 Å R-free 0.219 |
| 5J5B Structure of the WT E coli ribosome bound to tetracycline Deposited 2016-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain CJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 202 PG4 TETRAETHYLENE GLYCOL × 1 TAC TETRACYCLINE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；PEG 8000, Spermidine, Putrescine, Ammonium Chloride, Magnesium Chloride, MES pH 6.5
|
Resolution 2.80 Å R-free 0.219 |
| 5J7L Structure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracycline Deposited 2016-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 268 PG4 TETRAETHYLENE GLYCOL × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 14 PUT 1,4-DIAMINOBUTANE × 16 TAC TETRACYCLINE × 2 ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 11 EDO 1,2-ETHANEDIOL × 12 PGE TRIETHYLENE GLYCOL × 9 SPD SPERMIDINE × 4 1PE PENTAETHYLENE GLYCOL × 2 ACY ACETIC ACID × 3 GUN GUANINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；PEG 8k, Spermidine, Putrescine, Ammonium Chloride, Magnesium Chloride, MES pH 6.5
|
Resolution 3.00 Å R-free 0.193 |
| 5J7L Structure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracycline Deposited 2016-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain CJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 204 PG4 TETRAETHYLENE GLYCOL × 1 TAC TETRACYCLINE × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；PEG 8k, Spermidine, Putrescine, Ammonium Chloride, Magnesium Chloride, MES pH 6.5
|
Resolution 3.00 Å R-free 0.193 |
| 5J88 Structure of the E coli 70S ribosome with the U1060A mutation in 16S rRNA Deposited 2016-04-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DJ
8–142（135 aa）
|
Not recorded | MG MAGNESIUM ION × 266 PG4 TETRAETHYLENE GLYCOL × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 14 PUT 1,4-DIAMINOBUTANE × 16 ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 11 EDO 1,2-ETHANEDIOL × 12 PGE TRIETHYLENE GLYCOL × 9 SPD SPERMIDINE × 4 1PE PENTAETHYLENE GLYCOL × 2 ACY ACETIC ACID × 3 GUN GUANINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；PEG 8k, Spermidine, Putrescine, Ammonium Chloride, Magnesium Chloride, MES pH 6.5
|
Resolution 3.32 Å R-free 0.219 |
| 5J88 Structure of the E coli 70S ribosome with the U1060A mutation in 16S rRNA Deposited 2016-04-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain CJ
8–142（135 aa）
|
Not recorded | MG MAGNESIUM ION × 200 PG4 TETRAETHYLENE GLYCOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；PEG 8k, Spermidine, Putrescine, Ammonium Chloride, Magnesium Chloride, MES pH 6.5
|
Resolution 3.32 Å R-free 0.219 |
| 5J8A Structure of the E coli 70S ribosome with the U1052G mutation in 16S rRNA bound to tigecycline Deposited 2016-04-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DJ
8–142（135 aa）
|
Not recorded | MG MAGNESIUM ION × 268 PG4 TETRAETHYLENE GLYCOL × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 14 PUT 1,4-DIAMINOBUTANE × 16 T1C TIGECYCLINE × 1 ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 11 EDO 1,2-ETHANEDIOL × 12 PGE TRIETHYLENE GLYCOL × 9 SPD SPERMIDINE × 4 1PE PENTAETHYLENE GLYCOL × 2 ACY ACETIC ACID × 3 GUN GUANINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；PEG 8k, Spermidine, Putrescine, Ammonium Chloride, MAgnesium Chloride, MPD, MES pH 6.5
|
Resolution 3.10 Å R-free 0.192 |
| 5J8A Structure of the E coli 70S ribosome with the U1052G mutation in 16S rRNA bound to tigecycline Deposited 2016-04-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain CJ
8–142（135 aa）
|
Not recorded | MG MAGNESIUM ION × 204 PG4 TETRAETHYLENE GLYCOL × 1 T1C TIGECYCLINE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；PEG 8k, Spermidine, Putrescine, Ammonium Chloride, MAgnesium Chloride, MPD, MES pH 6.5
|
Resolution 3.10 Å R-free 0.192 |
| 5J91 Structure of the Wild-type 70S E coli ribosome bound to Tigecycline Deposited 2016-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 267 PG4 TETRAETHYLENE GLYCOL × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 14 PUT 1,4-DIAMINOBUTANE × 16 T1C TIGECYCLINE × 1 ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 11 EDO 1,2-ETHANEDIOL × 12 PGE TRIETHYLENE GLYCOL × 9 SPD SPERMIDINE × 4 1PE PENTAETHYLENE GLYCOL × 2 ACY ACETIC ACID × 3 GUN GUANINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG 8k, Spermidine, Putrescine, Ammonium Chloride, MAgnesium Chloride, MPD, MES pH 6.5
|
Resolution 2.96 Å R-free 0.221 |
| 5J91 Structure of the Wild-type 70S E coli ribosome bound to Tigecycline Deposited 2016-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain CJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 202 PG4 TETRAETHYLENE GLYCOL × 1 T1C TIGECYCLINE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG 8k, Spermidine, Putrescine, Ammonium Chloride, MAgnesium Chloride, MPD, MES pH 6.5
|
Resolution 2.96 Å R-free 0.221 |
| 5JC9 Structure of the Escherichia coli ribosome with the U1052G mutation in the 16S rRNA Deposited 2016-04-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric |
Chain DJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 267 PG4 TETRAETHYLENE GLYCOL × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 14 PUT 1,4-DIAMINOBUTANE × 16 ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 11 EDO 1,2-ETHANEDIOL × 12 PGE TRIETHYLENE GLYCOL × 9 SPD SPERMIDINE × 4 1PE PENTAETHYLENE GLYCOL × 2 ACY ACETIC ACID × 3 GUN GUANINE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG 8k, Spermidine, Putrescine, Ammonium Chloride, MAgnesium Chloride, MPD, MES
|
Resolution 3.03 Å R-free 0.200 |
| 5JC9 Structure of the Escherichia coli ribosome with the U1052G mutation in the 16S rRNA Deposited 2016-04-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric |
Chain CJ
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 202 PG4 TETRAETHYLENE GLYCOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG 8k, Spermidine, Putrescine, Ammonium Chloride, MAgnesium Chloride, MPD, MES
|
Resolution 3.03 Å R-free 0.200 |
| 5JTE Cryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNA Deposited 2016-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 58-meric |
Chain BI
1–142（142 aa）
|
Not recorded | LYS LYSINE × 1 ERY ERYTHROMYCIN A × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 5JU8 Cryo-EM structure of an ErmBL-stalled ribosome in complex with P-, and E-tRNA Deposited 2016-05-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain BI
1–142（142 aa）
|
Not recorded | ERY ERYTHROMYCIN A × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 5KCR Cryo-EM structure of the Escherichia coli 70S ribosome in complex with antibiotic Avilamycin C, mRNA and P-site tRNA at 3.6A resolution Deposited 2016-06-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric |
Chain 1K
1–142（142 aa）
|
Not recorded | 6UQ (2R,3S,4R,6S)-4-hydroxy-6-{[(2R,3aR,4R,4'R,5'S,6S,6'R,7aR)-4'-hydroxy-6-{[(2S,3R,4R,5S,6R)-3-hydroxy-2-{[(2R,3S,4S,5S,6S)-4-hydroxy-6-({(2R,3aS,3a'R,6S,6'R,7R,7'R,7aR,7a'R)-7'-hydroxy-7'-[(1S)-1-hydroxyethyl]-6'-methyl-7-[(2-methylpropanoyl)oxy]octahydro-4H-2,4'-spirobi[[1,3]dioxolo[4,5-c]pyran]-6-yl}oxy)-5-methoxy-2-(methoxymethyl)tetrahydro-2H-pyran-3-yl]oxy}-5-methoxy-6-methyltetrahydro-2H-pyran-4-yl]oxy}-4,6',7a-trimethyloctahydro-4H-spiro[1,3-dioxolo[4,5-c]pyran-2,2'-pyran]-5'-yl]oxy}-2-methyltetrahydro-2H-pyran-3-yl 3,5-dichloro-4-hydroxy-2-methoxy-6-methylbenzoate (non-preferred name) × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
X-ray crystallization conditions
pH 7.4
|
Resolution 3.60 Å |
| 5KCS Cryo-EM structure of the Escherichia coli 70S ribosome in complex with antibiotic Evernimycin, mRNA, TetM and P-site tRNA at 3.9A resolution Deposited 2016-06-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain 1K
1–142（142 aa）
|
Not recorded | EVN (2R,3R,4R,6S)-6-{[(2R,3aR,4R,4'R,5'S,6S,6'R,7S,7aR)-6-{[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5S,6S)-6-({(2R,3aS,3a'R,6S,7R,7' R,7aS,7a'S)-7'-[(2,4-dihydroxy-6-methylbenzoyl)oxy]-7-hydroxyoctahydro-4H-2,4'-spirobi[[1,3]dioxolo[4,5-c]pyran]-6-yl}ox y)-4-hydroxy-5-methoxy-2-(methoxymethyl)tetrahydro-2H-pyran-3-yl]oxy}-3-hydroxy-5-methoxy-6-methyltetrahydro-2H-pyran-4- yl]oxy}-4',7-dihydroxy-4,6',7a-trimethyloctahydro-4H-spiro[1,3-dioxolo[4,5-c]pyran-2,2'-pyran]-5'-yl]oxy}-4-{[(2R,4S,5R, 6S)-5-methoxy-4,6-dimethyl-4-nitrotetrahydro-2H-pyran-2-yl]oxy}-2-methyltetrahydro-2H-pyran-3-yl 3,5-dichloro-4-hydroxy-2-methoxy-6-methylbenzoate (non-preferred name) × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 5KPS Structure of RelA bound to ribosome in absence of A/R tRNA (Structure I) Deposited 2016-07-05 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Apply 2 uL sample and blot 4 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).
|
Resolution 3.90 Å |
| 5KPV Structure of RelA bound to ribosome in presence of A/R tRNA (Structure II) Deposited 2016-07-05 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain H
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Apply 2 uL sample and blot 4 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).
|
Resolution 4.10 Å |
| 5KPW Structure of RelA bound to ribosome in presence of A/R tRNA (Structure III) Deposited 2016-07-05 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain H
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Apply 2 uL sample and blot 4 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).
|
Resolution 3.90 Å |
| 5KPX Structure of RelA bound to ribosome in presence of A/R tRNA (Structure IV) Deposited 2016-07-05 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain H
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Apply 2 uL sample and blot 4 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).
|
Resolution 3.90 Å |
| 5L3P Cryo-EM structure of stringent response factor RelA bound to ErmCL-stalled ribosome complex Deposited 2016-05-24 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain K
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 5LZA Structure of the 70S ribosome with SECIS-mRNA and P-site tRNA (Initial complex, IC) Deposited 2016-09-29 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric |
Chain I
2–142（141 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM Hepes-KOH, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6mM spermine, 0.4mM spermidine, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 5LZB Structure of SelB-Sec-tRNASec bound to the 70S ribosome in the initial binding state (IB) Deposited 2016-09-29 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain I
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 SEC SELENOCYSTEINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM Hepes-KOH, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6mM spermine, 0.4mM spermidine, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.30 Å |
| 5LZC Structure of SelB-Sec-tRNASec bound to the 70S ribosome in the codon reading state (CR) Deposited 2016-09-29 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain I
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 SEC SELENOCYSTEINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM Hepes-KOH, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6mM spermine, 0.4mM spermidine, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 5LZD Structure of SelB-Sec-tRNASec bound to the 70S ribosome in the GTPase activated state (GA) Deposited 2016-09-29 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain I
2–142（141 aa）
|
Not recorded | CL CHLORIDE ION × 1 MG MAGNESIUM ION × 147 FME N-FORMYLMETHIONINE × 1 SEC SELENOCYSTEINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM Hepes-KOH, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6mM spermine, 0.4mM spermidine, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 5LZE Structure of the 70S ribosome with Sec-tRNASec in the classical pre-translocation state (C) Deposited 2016-09-29 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric |
Chain I
2–142（141 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM Hepes-KOH, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 5LZF Structure of the 70S ribosome with fMetSec-tRNASec in the hybrid pre-translocation state (H) Deposited 2016-09-29 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain I
2–142（141 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM Hepes-KOH, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6mM spermine, 0.4mM spermidine, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 5MDV Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state) Deposited 2016-11-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 440 FME N-FORMYLMETHIONINE × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.97 Å |
| 5MDW Structure of ArfA(A18T) and RF2 bound to the 70S ribosome (pre-accommodated state) Deposited 2016-11-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 438 FME N-FORMYLMETHIONINE × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 5MDY Structure of ArfA and TtRF2 bound to the 70S ribosome (pre-accommodated state) Deposited 2016-11-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 62-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 450 FME N-FORMYLMETHIONINE × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 5MDZ Structure of the 70S ribosome (empty A site) Deposited 2016-11-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 437 FME N-FORMYLMETHIONINE × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 5NCO Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome Deposited 2017-03-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 40-meric |
Chain J
8–141（134 aa）
|
Not recorded | ZN ZINC ION × 1 ALF TETRAFLUOROALUMINATE ION × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 5NP6 70S structure prior to bypassing Deposited 2017-04-13 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric |
Chain g
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 5NWY 2.9 A cryo-EM structure of VemP-stalled ribosome-nascent chain complex Deposited 2017-05-08 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain V
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 5O2R Cryo-EM structure of the proline-rich antimicrobial peptide Api137 bound to the terminating ribosome Deposited 2017-05-22 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 5U4I Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome Deposited 2016-12-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 124 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 5UYK 70S ribosome bound with cognate ternary complex not base-paired to A site codon (Structure I) Deposited 2017-02-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric |
Chain 11
2–142（141 aa）
|
Not recorded | GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；2 uL of complex was applied to each grid. After a 10-second incubation, the grids were blotted for 2 to 4 seconds.
|
Resolution 3.90 Å |
| 5UYL 70S ribosome bound with cognate ternary complex base-paired to A site codon (Structure II) Deposited 2017-02-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric |
Chain 11
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；2 uL of complex was applied to each grid. After a 10-second incubation, the grids were blotted for 2 to 4 seconds.
|
Resolution 3.60 Å |
| 5UYM 70S ribosome bound with cognate ternary complex base-paired to A site codon, closed 30S (Structure III) Deposited 2017-02-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric |
Chain 11
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 383 ZN ZINC ION × 2 FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；2 uL of complex was applied to each grid. After a 10-second incubation, the grids were blotted for 2 to 4 seconds.
|
Resolution 3.20 Å |
| 5UYN 70S ribosome bound with near-cognate ternary complex not base-paired to A site codon (Structure I-nc) Deposited 2017-02-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric |
Chain 11
2–142（141 aa）
|
Not recorded | GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；2 uL of complex was applied to each grid. After a 10-second incubation, the grids were blotted for 2 to 4 seconds.
|
Resolution 4.00 Å |
| 5UYP 70S ribosome bound with near-cognate ternary complex base-paired to A site codon, open 30S (Structure II-nc) Deposited 2017-02-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric |
Chain 11
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 LYS LYSINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；2 uL of complex was applied to each grid. After a 10-second incubation, the grids were blotted for 2 to 4 seconds.
|
Resolution 3.90 Å |
| 5UYQ 70S ribosome bound with near-cognate ternary complex base-paired to A site codon, closed 30S (Structure III-nc) Deposited 2017-02-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric |
Chain 11
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 LYS LYSINE × 1 MG MAGNESIUM ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；2 uL of complex was applied to each grid. After a 10-second incubation, the grids were blotted for 2 to 4 seconds.
|
Resolution 3.80 Å |
| 5WDT 70S ribosome-EF-Tu H84A complex with GppNHp Deposited 2017-07-06 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain I
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 MG MAGNESIUM ION × 1904 K POTASSIUM ION × 5 PHE PHENYLALANINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；5 second blot time,
no wait time
|
Resolution 3.00 Å |
| 5WE4 70S ribosome-EF-Tu wt complex with GppNHp Deposited 2017-07-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain I
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 1618 K POTASSIUM ION × 1 FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；5 second blot time,
no wait time
|
Resolution 3.10 Å |
| 5WE6 70S ribosome-EF-Tu H84A complex with GTP and cognate tRNA Deposited 2017-07-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain I
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 MG MAGNESIUM ION × 662 K POTASSIUM ION × 8 PHE PHENYLALANINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；5 second blot time,
no wait time
|
Resolution 3.40 Å |
| 5WFK 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C3) Deposited 2017-07-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain I
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 MG MAGNESIUM ION × 1413 K POTASSIUM ION × 1 PHE PHENYLALANINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；5 second blot time,
no wait time
|
Resolution 3.40 Å |
| 6BU8 70S ribosome with S1 domains 1 and 2 (Class 1) Deposited 2017-12-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric |
Chain 11
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；2 uL of complex was applied to each grid. After a 10-second incubation, the grids were blotted for 2 to 4 seconds.
|
Resolution 3.50 Å |
| 6BY1 E. coli pH03H9 complex Deposited 2017-12-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric |
Chain CI
71–142（72 aa）
|
Not recorded | MG MAGNESIUM ION × 225 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；PEG 2000, PEP629, potassium thiocyanate, tris acetate
|
Resolution 3.94 Å R-free 0.269 |
| 6BY1 E. coli pH03H9 complex Deposited 2017-12-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 55-meric |
Chain DI
71–142（72 aa）
|
Not recorded | MG MAGNESIUM ION × 220 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；PEG 2000, PEP629, potassium thiocyanate, tris acetate
|
Resolution 3.94 Å R-free 0.269 |
| 6C4I Conformation of methylated GGQ in the peptidyl transferase center during translation termination Deposited 2018-01-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 317 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Grids were blotted for 3.5 seconds.
|
Resolution 3.24 Å |
| 6GWT Cryo-EM structure of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State I) Deposited 2018-06-25 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
2–142（141 aa）
|
Not recorded | GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Solutions were preapred fresh and filtered previous to usage.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6GXM Cryo-EM structure of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State II) Deposited 2018-06-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
2–142（141 aa）
|
Not recorded | GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Solutions were preapred fresh and filtered previous to usage.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6GXN Cryo-EM structure of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State III) Deposited 2018-06-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
2–142（141 aa）
|
Not recorded | GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Solutions were preapred fresh and filtered previous to usage.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6GXO Cryo-EM structure of a rotated E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and P/E-tRNA (State IV) Deposited 2018-06-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
2–142（141 aa）
|
Not recorded | GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Solutions were preapred fresh and filtered previous to usage.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6GXP Cryo-EM structure of a rotated E. coli 70S ribosome in complex with RF3-GDPCP(RF3-only) Deposited 2018-06-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric |
Chain I
2–142（141 aa）
|
Not recorded | GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Solutions were preapred fresh and filtered previous to usage.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 6HRM E. coli 70S d2d8 stapled ribosome Deposited 2018-09-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 53-meric |
Chain I
6–140（135 aa）
|
Not recorded | MG MAGNESIUM ION × 436 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.96 Å |
| 6I0Y TnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel Deposited 2018-10-26 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 36-meric |
Chain I
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 143 ZN ZINC ION × 1 TRP TRYPTOPHAN × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 6I7V Ribosomal protein paralogs bL31 and bL36 Deposited 2018-11-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 99 PDB declaration: 105-meric |
Chain CJ
2–142（141 aa）
Chain DJ
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 453 PGE TRIETHYLENE GLYCOL × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 13 PG4 TETRAETHYLENE GLYCOL × 5 SPD SPERMIDINE × 3 PUT 1,4-DIAMINOBUTANE × 7 1PE PENTAETHYLENE GLYCOL × 2 ACY ACETIC ACID × 3 PEG DI(HYDROXYETHYL)ETHER × 9 EDO 1,2-ETHANEDIOL × 12 GUN GUANINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KSCN
|
Resolution 2.90 Å R-free 0.255 |
| 6Q97 Structure of tmRNA SmpB bound in A site of E. coli 70S ribosome Deposited 2018-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric |
Chain I
6–140（135 aa）
|
Not recorded | MG MAGNESIUM ION × 439 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6Q98 Structure of tmRNA SmpB bound in P site of E. coli 70S ribosome Deposited 2018-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 57-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 429 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 6Q9A Structure of tmRNA SmpB bound past E site of E. coli 70S ribosome Deposited 2018-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
6–140（135 aa）
|
Not recorded | MG MAGNESIUM ION × 437 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6S0K Ribosome nascent chain in complex with SecA Deposited 2019-06-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 68 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.10 Å |
| 6WD6 Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-C2) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6WDB Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure IV-A) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6WDC Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure IV-B) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 6WDD Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure V-A) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 6WDE Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure V-B) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | PHE PHENYLALANINE × 1 MET METHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 6WDF Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure VI-A) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric |
Chain i
2–142（141 aa）
|
Not recorded | PHE PHENYLALANINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 6WDG Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure VI-B) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric |
Chain i
2–142（141 aa）
|
Not recorded | PHE PHENYLALANINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 6WDH Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure IV-B1) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 6WDI Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure IV-B2) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6WDJ Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure V-A1) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6WDK Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure V-A2) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 6WDL Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure V-B1) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6WDM Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Non-cognate Structure V-B2) Deposited 2020-03-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | PHE PHENYLALANINE × 1 FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 6WNT 50S ribosomal subunit without free 5S rRNA and perturbed PTC Deposited 2020-04-23 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 31-meric |
Chain i
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 6WNV 70S ribosome without free 5S rRNA and with a perturbed PTC Deposited 2020-04-23 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 52-meric |
Chain i
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6WNW Active 70S ribosome without free 5S rRNA and bound with A- and P- tRNA Deposited 2020-04-23 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric |
Chain i
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 6XZ7 E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet). Deposited 2020-02-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 33-meric |
Chain I
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 178 DI0 Dirithromycin × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.10 Å |
| 6XZA E. coli 70S ribosome in complex with dirithromycin, and deacylated tRNA(iMet) (focused classification). Deposited 2020-02-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric |
Chain I2
8–141（134 aa）
|
Not recorded | DI0 Dirithromycin × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 6XZB E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification). Deposited 2020-02-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric |
Chain I2
8–141（134 aa）
|
Not recorded | DI0 Dirithromycin × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.54 Å |
| 6YSR Structure of the P+9 stalled ribosome complex Deposited 2020-04-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 332 ZN ZINC ION × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；50 mM HEPES, 30 mM KCl, 7 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 3.10 Å |
| 6YSS Structure of the P+9 ArfB-ribosome complex in the post-hydrolysis state Deposited 2020-04-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 387 ZN ZINC ION × 2 NA SODIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；50 mM HEPES, 30 mM KCl, 7 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 2.60 Å |
| 6YST Structure of the P+9 ArfB-ribosome complex with P/E hybrid tRNA in the post-hydrolysis state Deposited 2020-04-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 253 ZN ZINC ION × 2 NA SODIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；50 mM HEPES, 30 mM KCl, 7 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 3.20 Å |
| 6YSU Structure of the P+0 ArfB-ribosome complex in the post-hydrolysis state Deposited 2020-04-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 356 ZN ZINC ION × 1 NA SODIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；50 mM HEPES, 30 mM KCl, 7 mM MgCl2, 0.1 % w/v DDM
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6ZTJ E. coli 70S-RNAP expressome complex in NusG-coupled state (38 nt intervening mRNA) Deposited 2020-07-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 66-meric |
Chain BJ
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 479 PHE PHENYLALANINE × 1 ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7ABZ Structure of pre-accomodated trans-translation complex on E. coli stalled ribosome. Deposited 2020-09-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 192 KIR KIRROMYCIN × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 3.5 seconds before plunging
|
Resolution 3.21 Å |
| 7BL2 pre-50S-ObgE particle state 1 Deposited 2021-01-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7BL3 pre-50S-ObgE particle state 2 Deposited 2021-01-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric |
Chain I
1–142（142 aa）
|
Not recorded | ZN ZINC ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7BL5 pre-50S-ObgE particle Deposited 2021-01-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 35-meric |
Chain I
1–142（142 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7BV8 Mature 50S ribosomal subunit from RrmJ knock out E.coli strain Deposited 2020-04-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric |
Chain J
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Solutions were made fresh form concentrated to avoid microbial contamination.
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2 seconds before plunging
|
Resolution 3.14 Å |
| 7D6Z Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factor Deposited 2020-10-02 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7D80 Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase, trigger factor, and methionine aminopeptidase Deposited 2020-10-06 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric |
Chain h
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7JSZ ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a partial A-site codon (+2-IV) Deposited 2020-08-16 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric |
Chain i
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7JT3 Rotated 70S ribosome stalled on long mRNA with ArfB-1 and ArfB-2 bound in the A site (+9-IV) Deposited 2020-08-17 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain i
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7K50 Pre-translocation non-frameshifting(CCA-A) complex (Structure I) Deposited 2020-09-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Blotting force 9, blotted for 4 seconds
|
Resolution 3.40 Å |
| 7K51 Mid-translocated non-frameshifting(CCA-A) complex with EF-G and GDPCP (Structure II) Deposited 2020-09-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PRO PROLINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Blotting force 9, blotted for 4 seconds
|
Resolution 3.50 Å |
| 7K52 Near post-translocated non-frameshifting(CCA-A) complex with EF-G and GDPCP (Structure III) Deposited 2020-09-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PRO PROLINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blotting force 9, blotted for 4 seconds
|
Resolution 3.40 Å |
| 7K53 Pre-translocation +1-frameshifting(CCC-A) complex (Structure I-FS) Deposited 2020-09-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 59-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Blotting force 9, blotted for 4 seconds
|
Resolution 3.20 Å |
| 7K54 Mid-translocated +1-frameshifting(CCC-A) complex with EF-G and GDPCP (Structure II-FS) Deposited 2020-09-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PRO PROLINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Blotting force 9, blotted for 4 seconds
|
Resolution 3.20 Å |
| 7K55 Near post-translocated +1-frameshifting(CCC-A) complex with EF-G and GDPCP (Structure III-FS) Deposited 2020-09-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PRO PROLINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blotting force 9, blotted for 4 seconds
|
Resolution 3.30 Å |
| 7LV0 Pre-translocation rotated ribosome +1-frameshifting(CCC-A) complex (Structure Irot-FS) Deposited 2021-02-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PRO PROLINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Blotting force 9, blotted for 4 seconds
|
Resolution 3.20 Å |
| 7N1P Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation Deposited 2021-05-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain LK
1–142（142 aa）
|
Not recorded | PUT 1,4-DIAMINOBUTANE × 18 MG MAGNESIUM ION × 405 ZN ZINC ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 SPD SPERMIDINE × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.33 Å |
| 7N2C Elongating 70S ribosome complex in a fusidic acid-stalled intermediate state of translocation bound to EF-G(GDP) (INT2) Deposited 2021-05-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 61-meric |
Chain LK
1–142（142 aa）
|
Not recorded | PUT 1,4-DIAMINOBUTANE × 21 MG MAGNESIUM ION × 197 ZN ZINC ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 SPD SPERMIDINE × 3 FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.72 Å |
| 7N2V Elongating 70S ribosome complex in a spectinomycin-stalled intermediate state of translocation bound to EF-G in an active, GTP conformation (INT1) Deposited 2021-05-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain LK
1–142（142 aa）
|
Not recorded | SCM SPECTINOMYCIN × 3 PUT 1,4-DIAMINOBUTANE × 17 MG MAGNESIUM ION × 344 ZN ZINC ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 SPD SPERMIDINE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.54 Å |
| 7NWT Initiated 70S ribosome in complex with 2A protein from encephalomyocarditis virus (EMCV) Deposited 2021-03-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 59-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 437 FME N-FORMYLMETHIONINE × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Initiated 70S ribosomes in 50 mM Tris-HCl pH 7.5, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2 were diluted tenfold into 20 mM HEPES pH 7.5, 100 mM potassium acetate, 1.5 mM MgCl2, 2.0 mM DTT. 2A protein was dialysed (3K MWCO, 277K, 16 h) into the same buffer.
Crosslinking reactions of 50 microliters comprising 75 nM ribosomes, 3.0 micromolar 2A and 2.0 mM bis(sulfosuccinimidyl)suberate (BS3) were performed on ice (30 min) immediately prior to grid preparation.
cryo-EM vitrification conditions
Cryogen ETHANE；Quantifoil R 2/2 400-mesh copper supports were coated with an additional ~ 60 angstrom layer of amorphous, evaporated carbon by flotation and thoroughly dried before use. Grids were made hydrophilic by glow-discharge in air for 30 s. Three microliters of crosslinking reaction was applied to grids which were then blotted for 4.5 s and vitrified by plunging into liquid ethane using a Vitrobot MK IV (FEI) at 277K, 100% relative humidity.
|
Resolution 2.66 Å |
| 7PJS Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) Deposited 2021-08-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 363 ZN ZINC ION × 2 NA SODIUM ION × 2 AM2 APRAMYCIN × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 2.35 Å |
| 7PJT Structure of the 70S ribosome with tRNAs in hybrid state 1 (H1) Deposited 2021-08-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | ZN ZINC ION × 2 AM2 APRAMYCIN × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 6.00 Å |
| 7PJV Structure of the 70S-EF-G-GDP-Pi ribosome complex with tRNAs in hybrid state 1 (H1-EF-G-GDP-Pi) Deposited 2021-08-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 369 ZN ZINC ION × 2 NA SODIUM ION × 2 AM2 APRAMYCIN × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 3.10 Å |
| 7PJW Structure of the 70S-EF-G-GDP-Pi ribosome complex with tRNAs in hybrid state 2 (H2-EF-G-GDP-Pi) Deposited 2021-08-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain I
1–142（142 aa）
|
Not recorded | AM2 APRAMYCIN × 1 PO4 PHOSPHATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 4.00 Å |
| 7PJX Structure of the 70S-EF-G-GDP ribosome complex with tRNAs in hybrid state 1 (H1-EF-G-GDP) Deposited 2021-08-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain I
1–142（142 aa）
|
Not recorded | AM2 APRAMYCIN × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 6.50 Å |
| 7PJY Structure of the 70S-EF-G-GDP ribosome complex with tRNAs in chimeric state 1 (CHI1-EF-G-GDP) Deposited 2021-08-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 318 ZN ZINC ION × 2 NA SODIUM ION × 1 AM2 APRAMYCIN × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 3.10 Å |
| 7PJZ Structure of the 70S-EF-G-GDP ribosome complex with tRNAs in chimeric state 2 (CHI2-EF-G-GDP) Deposited 2021-08-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain I
1–142（142 aa）
|
Not recorded | ZN ZINC ION × 1 AM2 APRAMYCIN × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 6.00 Å |
| 7QG8 Structure of the collided E. coli disome - VemP-stalled 70S ribosome Deposited 2021-12-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric |
Chain V
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 2 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.97 Å |
| 7QGH Structure of the E. coli disome - collided 70S ribosome Deposited 2021-12-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain V
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 2 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.48 Å |
| 7QGN Structure of the SmrB-bound E. coli disome - stalled 70S ribosome Deposited 2021-12-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain V
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 2 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.37 Å |
| 7QGR Structure of the SmrB-bound E. coli disome - collided 70S ribosome Deposited 2021-12-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain V
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 2 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.70 Å |
| 7SS9 Late translocation intermediate with EF-G partially dissociated (Structure V) Deposited 2021-11-10 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric |
Chain i
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7SSD Mid translocation intermediate with EF-G bound with GDP (Structure IV) Deposited 2021-11-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain i
1–142（142 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7SSL Pre translocation intermediate with EF-G bound to GDP and Pi (Structure III) Deposited 2021-11-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7SSN Pre translocation 70S ribosome with A/P* and P/E tRNA (Structure II-B) Deposited 2021-11-11 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 54-meric |
Chain i
2–142（141 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7SSO Pre translocation 70S ribosome with A/A and P/E tRNA (Structure II-A) Deposited 2021-11-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain i
2–142（141 aa）
|
Not recorded | FME N-FORMYLMETHIONINE × 1 PRO PROLINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7SSW Late translocation intermediate with EF-G dissociated (Structure VI) Deposited 2021-11-11 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric |
Chain i
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7ST2 Post translocation, non-rotated 70S ribosome with EF-G dissociated (Structure VII) Deposited 2021-11-11 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain i
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7ST6 Pre translocation, non-rotated 70S ribosome (Structure I) Deposited 2021-11-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric |
Chain i
1–142（142 aa）
|
Not recorded | PRO PROLINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7ST7 Pre translocation intermediate stalled with viomycin and bound with EF-G in a GDP and Pi state (Structure III-vio) Deposited 2021-11-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain i
2–142（141 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7UG7 70S ribosome complex in an intermediate state of translocation bound to EF-G(GDP) stalled by Argyrin B Deposited 2022-03-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 60-meric |
Chain LK
1–142（142 aa）
|
Not recorded | PUT 1,4-DIAMINOBUTANE × 11 MG MAGNESIUM ION × 404 SPD SPERMIDINE × 2 ZN ZINC ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 FME N-FORMYLMETHIONINE × 1 PHE PHENYLALANINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.58 Å |
| 7YLA Cryo-EM structure of 50S-HflX complex Deposited 2022-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric |
Chain Q
8–141（134 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 3 NA SODIUM ION × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.52 Å |
| 8FIZ Cryo-EM structure of E. coli 70S Ribosome containing mRNA and tRNA (in the transcription-translation complex) Deposited 2022-12-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain BL
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8FZD Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with apoRF3, RF1, P- and E-site tRNAPhe (Composite state I-B) Deposited 2023-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 581 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；5 mM Tris-HCl, 60 mM NH4Cl, 10 mM MgCl2, 6 mM B-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8FZE Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF1, P- and E-site tRNAPhe (State I-A) Deposited 2023-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 570 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；5 mM Tris-HCl, 60 mM NH4Cl, 10 mM MgCl2, 6 mM B-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8FZF Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (Composite state I-C) Deposited 2023-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 384 G4P GUANOSINE-5',3'-TETRAPHOSPHATE × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；5 mM Tris-HCl, 60 mM NH4Cl, 10 mM MgCl2, 6 mM B-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8FZG Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF3-GDPCP, RF1, P- and E-site tRNAPhe (Composite state II-A) Deposited 2023-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 428 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；5 mM Tris-HCl, 60 mM NH4Cl, 10 mM MgCl2, 6 mM B-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8FZH Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF1, P- and E-site tRNAPhe (State II-D) Deposited 2023-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 595 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；5 mM Tris-HCl, 60 mM NH4Cl, 10 mM MgCl2, 6 mM B-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8FZI Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-B) Deposited 2023-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 737 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；5 mM Tris-HCl, 60 mM NH4Cl, 10 mM MgCl2, 6 mM B-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8FZJ Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-C) Deposited 2023-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 757 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；5 mM Tris-HCl, 60 mM NH4Cl, 10 mM MgCl2, 6 mM B-mercaptoethanol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8G7P Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the cognate AUA codon (Structure I) Deposited 2023-02-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain J
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 876 K POTASSIUM ION × 2 ILE ISOLEUCINE × 2 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8G7Q Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the near-cognate AUG codon (Structure II) Deposited 2023-02-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric |
Chain J
1–142（142 aa）
|
Not recorded | PAR PAROMOMYCIN × 1 MG MAGNESIUM ION × 950 ILE ISOLEUCINE × 2 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8P16 E167K RF2 on E. coli 70S release complex with UGG (Structure I) Deposited 2023-05-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 330 SPD SPERMIDINE × 13 K POTASSIUM ION × 128 PUT 1,4-DIAMINOBUTANE × 13 SPM SPERMINE × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；HEPES-polymix buffer (pH-7.5)
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.77 Å |
| 8P17 E167K RF2 on E. coli 70S release complex with UGG (Structure II) Deposited 2023-05-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 325 SPD SPERMIDINE × 13 K POTASSIUM ION × 128 PUT 1,4-DIAMINOBUTANE × 13 SPM SPERMINE × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；HEPES-polymix buffer (pH-7.5)
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.78 Å |
| 8P18 E167K RF2 on E. coli 70S release complex with UGG (Structure III) Deposited 2023-05-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 321 SPD SPERMIDINE × 13 K POTASSIUM ION × 127 PUT 1,4-DIAMINOBUTANE × 13 SPM SPERMINE × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；HEPES-polymix buffer (pH-7.5)
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.77 Å |
| 8PEG Escherichia coli paused disome complex (queueing 70S non-rotated closed PRE state) Deposited 2023-06-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 61-meric |
Chain k
1–142（142 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 260 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；Withdrawn samples were spotted directly onto freshly glow-discharged holey carbon grids, blotted for 1-2 s, and flash frozen in liquid ethane using a Vitrobot Mark IV plunger (ThermoFisher Scientific) after a wait time of 40 s at 4 degrees Celcius.
|
Resolution 3.30 Å |
| 8PHJ cA4-bound Cami1 in complex with 70S ribosome Deposited 2023-06-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 61-meric |
Chain 6
1–142（142 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 241 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.67 Å |
| 8PKL Escherichia coli paused disome complex (leading 70S non-rotated closed PRE state) Deposited 2023-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric |
Chain k
1–142（142 aa）
|
Not recorded | ZN ZINC ION × 2 PUT 1,4-DIAMINOBUTANE × 2 SPD SPERMIDINE × 1 MG MAGNESIUM ION × 287 ALA ALANINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；Withdrawn samples were spotted directly onto freshly glow-discharged holey carbon grids, blotted for 1-2 s, and flash frozen in liquid ethane using a Vitrobot Mark IV plunger (ThermoFisher Scientific) after a wait time of 40 s at 4 degrees Celcius.
|
Resolution 3.09 Å |
| 8QK7 E167K RF2 on E. coli 70S release complex with UAA Deposited 2023-09-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 332 PUT 1,4-DIAMINOBUTANE × 21 K POTASSIUM ION × 126 SPD SPERMIDINE × 10 SPM SPERMINE × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；HEPES-polymix buffer (pH-7.5)
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.77 Å |
| 8UPO Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 66-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.50 Å |
| 8UPR Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.30 Å |
| 8UQL Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8UQM Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.30 Å |
| 8UQP Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8UR0 Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8URH Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.70 Å |
| 8URI Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 27 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.30 Å |
| 8URX Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 30 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Deposited 2023-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.60 Å |
| 8URY Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 30 nt long spacer, and fMet-tRNA in E-site and P-site of the ribosome Deposited 2023-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VKV Escherichia coli transcription-translation coupled complex (TTC-B) containing mRNA with a 33 nt long spacer, ops signal, RfaH, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8VL1 Escherichia coli transcription-translation loosely coupled complex (TTC-LC) containing mRNA with a 36 nt long spacer, ops signal, RfaH, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.30 Å |
| 8VOO Escherichia coli transcription-translation loosely coupled complex (TTC-LC) containing mRNA with a 39 nt long spacer, ops signal, RfaH, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8VOP Escherichia coli transcription-translation coupled complex (TTC-B) containing mRNA with a 36 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.00 Å |
| 8VOQ Escherichia coli transcription-translation loosely coupled complex (TTC-LC) containing mRNA with a 39 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.30 Å |
| 8VOR Escherichia coli transcription-translation loosely coupled complex (TTC-LC) containing mRNA with a 51 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8VOS Escherichia coli transcription-translation loosely coupled complex (TTC-LC) containing mRNA with a 60 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site Deposited 2024-01-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 8VS9 Endogenous trans-translation complex with tmRNA*SmpB in the P site and alanyl-tRNA in the A site and deacyl-tRNA in the E site of E. coli 70S ribosome Deposited 2024-01-23 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain L11
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8VSA Endogenous trans-translation complex with tmRNA*SmpB in the P site and alanyl-tRNA in the A site of E. coli 70S ribosome Deposited 2024-01-23 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain L11
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8Y5K E.coli transcription translation coupling complex in TTC-A state 2 containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 8Y5L E.coli transcription translation coupling complex in TTC-B state 1 (subclass1) containing mRNA with 30-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 67-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8Y5M E.coli transcription translation coupling complex in TTC-B state 2 containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8Y5N E.coli transcription translation coupling complex in TTC-A state 3 containing mRNA with 21-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 67-meric |
Chain i
1–142（142 aa）
|
Not recorded | GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8Y5O E.coli transcription translation coupling complex in TTC-B state 3 (subclass1) containing mRNA with 30-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 8Y5P E.coli transcription translation coupling complex in TTC-B state 4 (subclass 1) containing mRNA with 24-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 67-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.50 Å |
| 8Y5Q E.coli transcription translation coupling complex in TTC-B state 4 (subclass 2) containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and GDPCP Deposited 2024-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 59 PDB declaration: 66-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8Y5R E.coli Transcription translation coupling complex in TTC-B state 5 (subclass 1) containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and fusidic acid Deposited 2024-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 66-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8Y5S E.coli Transcription translation coupling complex in TTC-B state 5 (subclass 2) containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and GDPCP Deposited 2024-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 66-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8Y5T E.coli Transcription translation coupling complex in TTC-B state 5 (subclass 3) containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and fusidic acid Deposited 2024-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 66-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 8YDE E.coli transcription translation coupling complex in TTC-B state 1 (subclass 3) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 67-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.00 Å |
| 8YDF E.coli transcription translation coupling complex in TTC-B state 1 (subclass 2) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 67-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 8YDG E.coli transcription translation coupling complex in TTC-B state 3 (subclass2) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.10 Å |
| 8YDH E.coli transcription translation coupling complex in TTC-P state 1 (subclass1) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 67-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.55 Å |
| 8YDI E.coli transcription translation coupling complex in TTC-P state 1 (subclass 2) containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 67-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 8YDJ E.coli transcription translation coupling complex in TTC-P containing mRNA with 39-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin Deposited 2024-02-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain i
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.10 Å |
| 9GFT Structure of the HrpA-bound E. coli disome, Class I Deposited 2024-08-12 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 105 PDB declaration: 116-meric |
Chain Ad
1–142（142 aa）
Chain V
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9GGR Structure of the HrpA-bound E. coli disome, Class II Deposited 2024-08-14 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 106 PDB declaration: 117-meric |
Chain Ad
1–142（142 aa）
Chain V
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9MOR Damaged 70S ribosome with PrfH bound Deposited 2024-12-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 439 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.65 Å |
| 9MQ4 Damaged 70S ribosome with PrfH bound Deposited 2025-01-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 439 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.78 Å |
| 9NJF E. coli pre-elongation complex without an A-site tRNA with EQ2-YbiT in Non-hydrolytic 1/PtIM(a) conformation Deposited 2025-02-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric |
Chain 11
2–142（141 aa）
|
Not recorded | MG MAGNESIUM ION × 124 ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 NA SODIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9Q87 Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+ Deposited 2025-02-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 55-meric |
Chain 5
2–142（141 aa）
|
Not recorded | K POTASSIUM ION × 235 MG MAGNESIUM ION × 415 CU1 COPPER (I) ION × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.55 Å |
| 9RTU Structure of the 70S-EF-G(P610L)-GDP-Pi ribosome complex with tRNAs in hybrid state 1 (H1-EF-G(P610L)-GDP-Pi) Deposited 2025-07-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 369 ZN ZINC ION × 2 NA SODIUM ION × 2 AM2 APRAMYCIN × 3 PO4 PHOSPHATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 3.00 Å |
| 9RTV Structure of the 70S-EF-G(P610L)-GDP-Pi ribosome complex with tRNAs in hybrid state 2 (H2-EF-G(P610L)-GDP-Pi) Deposited 2025-07-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric |
Chain I
1–142（142 aa）
|
Not recorded | MG MAGNESIUM ION × 369 ZN ZINC ION × 2 NA SODIUM ION × 2 AM2 APRAMYCIN × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions
Cryogen ETHANE；Manual blotting & plunge-freezing
|
Resolution 3.60 Å |
| 9SS4 pre-50S ribosomal subunit in rimM-KO with RsfS (-H68) Deposited 2025-09-25 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 35-meric |
Chain BK
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9SS5 50S ribosomal subunit in rimM-KO with RsfS (+H68) Deposited 2025-09-25 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 34-meric |
Chain BK
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9SS6 70S ribosome from RimM-KO Deposited 2025-09-25 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric |
Chain BK
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 9XFK In situ structure of bacterial 50S ribosomes Deposited 2025-10-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric |
Chain Q
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 166 NA SODIUM ION × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 9XFL In vitro structure of bacterial 50S ribosomes Deposited 2025-10-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric |
Chain Q
8–141（134 aa）
|
Not recorded | MG MAGNESIUM ION × 176 NA SODIUM ION × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 9Y79 Escherichia coli transcription-translation loosely coupled complex (TTC-LC^walked) containing mRNA with a 39 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site Deposited 2025-09-09 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 60 PDB declaration: 68-meric |
Chain Y
1–142（142 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.20 Å |
284 other PDB entries and 329 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | RL11_ECOLI |
| Isoform | — |
| PDB entities | 7 |
| Chains and sequence ranges | Author chain G； PDBConstruct 1–141； UniProt 2–142 |
