50S ribosomal protein L7/L12
Escherichia coli
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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count | Chain A; UniProt 1–120 Chain B; UniProt 1–120 | Fragment:L7 dimer | No other associated polymer | SOLUTION NMR NMR measurement conditions:pH 6.9;303 K;Ionic strength (raw mmCIF value) 0.15;Pressure ambient NMR sample composition:1mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C | 90% H2O/10% D2O NMR sample composition:1mM L7 dimer U-15N; 50mM phosphate buffer; 99.9% D2O; 30 C | 99.9% D2O NMR sample composition:1mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C; Tobacco virus alignment medium | 90% H2O/10% D2O | Resolution not provided |
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 1RQU | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1CTF STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RIBOSOMAL PROTEIN L7/L12 FROM ESCHERICHIA COLI AT 1.7 ANGSTROMS Deposited 1986-09-02 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
47–120(74 aa)
|
Not recorded | SO4 SULFATE ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.70 Å |
| 1RQS NMR structure of C-terminal domain of ribosomal protein L7 from E.coli Deposited 2003-12-07 | Different construct Different mutation/modification Different oligomeric state | Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric |
Chain A
47–120(74 aa)
Fragment:C-Terminal Domain
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.9;303 K;Ionic strength (raw mmCIF value) 0.15;Pressure ambient
NMR sample composition
1mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C | 90% H2O/10% D2O
NMR sample composition
1mM L7 dimer U-15N; 50mM phosphate buffer; 99.9% D2O; 30 C | 99.9% D2O
NMR sample composition
1mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C; Tobacco virus alignment medium | 90% H2O/10% D2O
|
Resolution not provided |
| 1RQT NMR structure of dimeric N-terminal domain of ribosomal protein L7 from E.coli Deposited 2003-12-07 | Different construct Different experimental conditions | Assembly 1 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
1–37(37 aa)
Fragment:N-Terminal Domain
Chain B
1–37(37 aa)
Fragment:N-Terminal Domain
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.9;303 K;Ionic strength (raw mmCIF value) 0.15;Pressure ambient
NMR sample composition
1mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C | 90% H2O/10% D2O
NMR sample composition
1mM L7 dimer U-15N; 50mM phosphate buffer; 99.9% D2O; 30 C | 99.9% D2O
|
Resolution not provided |
| 1RQV Spatial model of L7 dimer from E.coli with one hinge region in helical state Deposited 2003-12-07 | Parsed fields agree | Assembly 1 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
1–120(120 aa)
Fragment:L7 dimer
Chain B
1–120(120 aa)
Fragment:L7 dimer
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.9;303 K;Ionic strength (raw mmCIF value) 0.15;Pressure ambient
NMR sample composition
1mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C | 90% H2O/10% D2O
NMR sample composition
1mM L7 dimer U-15N; 50mM phosphate buffer; 99.9% D2O; 30 C | 99.9% D2O
NMR sample composition
1mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C; Tobacco virus alignment medium | 90% H2O/10% D2O
|
Resolution not provided |
| 2BCW Coordinates of the N-terminal domain of ribosomal protein L11,C-terminal domain of ribosomal protein L7/L12 and a portion of the G' domain of elongation factor G, as fitted into cryo-em map of an Escherichia coli 70S*EF-G*GDP*fusidic acid complex Deposited 2005-10-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric |
Chain B
53–120(68 aa)
Fragment:C-terminal domain
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine;pH 7.5;20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine
cryo-EM vitrification conditions
RAPID-FREEZING IN LIQUID ETHANE
|
Resolution 11.20 Å |
| 3J7Z Structure of the E. coli 50S subunit with ErmCL nascent chain Deposited 2014-08-27 | 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 × 32 PDB declaration: 35-meric |
Chain 6
1–121(121 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 |
| 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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 46 PDB declaration: 52-meric |
Chain B3
2–120(119 aa)
Chain B5
2–120(119 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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 46 PDB declaration: 52-meric |
Chain B3
3–121(119 aa)
Chain B5
3–121(119 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 |
| 4V5M tRNA tranlocation on the 70S ribosome: the pre-translocational translocation intermediate TI(PRE) Deposited 2010-10-01 | 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 × 52 PDB declaration: 57-meric |
Chain BL
1–121(121 aa)
|
Not recorded | FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE;VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- VITROBOT (FEI)
|
Resolution 7.80 Å |
| 4V5N tRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST) Deposited 2010-10-21 | 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 × 52 PDB declaration: 57-meric |
Chain BL
1–121(121 aa)
|
Not recorded | FUA FUSIDIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM vitrification conditions
Cryogen ETHANE;VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- VITROBOT (FEI)
|
Resolution 7.60 Å |
| 4V7B Visualization of two tRNAs trapped in transit during EF-G-mediated translocation Deposited 2013-10-27 | 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 × 52 PDB declaration: 58-meric |
Chain B6
1–121(121 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 |
| 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 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 × 54 PDB declaration: 60-meric |
Chain AL
2–121(120 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 |
| 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 mutation/modification 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 BJ
1–121(121 aa)
Chain BK
1–121(121 aa)
Chain BL
1–121(121 aa)
Chain BM
1–121(121 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 |
| 4V9O Control of ribosomal subunit rotation by elongation factor G Deposited 2013-05-03 | 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 × 53 PDB declaration: 56-meric |
Chain A6
1–121(121 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 |
| 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 mutation/modification 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: 58-meric |
Chain 1L
1–121(121 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 |
| 6I0Y TnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel Deposited 2018-10-26 | 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 × 33 PDB declaration: 36-meric |
Chain 6
1–121(121 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 |
| 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer;Protein × 55 PDB declaration: 61-meric |
Chain LG
1–121(121 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 |
| 8PHJ cA4-bound Cami1 in complex with 70S ribosome Deposited 2023-06-20 | 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 × 54 PDB declaration: 61-meric |
Chain W
2–121(120 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 |
18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | RL7_ECOLI |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 1–120; UniProt 1–120 Author chain B; PDBConstruct 1–120; UniProt 1–120 |