← Back to search
1ctf

STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RIBOSOMAL PROTEIN L7/L12 FROM ESCHERICHIA COLI AT 1.7 ANGSTROMS

Method: X-RAY DIFFRACTION Dmax: 40.4 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBOSOMAL PROTEIN L7/L12

Escherichia coli

UniProt P0A7K2

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 47–120 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.70 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 1CTF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1RQS NMR structure of C-terminal domain of ribosomal protein L7 from E.coli Deposited 2003-12-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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 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 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
1RQU NMR structure of L7 dimer from E.coli Deposited 2003-12-07 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 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
1RQV Spatial model of L7 dimer from E.coli with one hinge region in helical state Deposited 2003-12-07 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 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 oligomeric state Different ligand/ion 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 1–74； UniProt 47–120

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1ctf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ctf
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1ctf
Deposition date deposition_date1986-09-02
Structure title titleSTRUCTURE OF THE C-TERMINAL DOMAIN OF THE RIBOSOMAL PROTEIN L7/L12 FROM ESCHERICHIA COLI AT 1.7 ANGSTROMS
Keywords keywordsRIBOSOMAL PROTEIN; RIBOSOMAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.65 Å
Radius of gyration Rg (electron density) rg_electron11.20 Å
Forward intensity I(0) i01123830.00
Molecular weight molecular_weight7026.0 kDa
Excluded volume excluded_volume8869 ų
Envelope volume envelope_volume9907 ų
Hydration-shell volume shell_volume7924 ų
Envelope diameter envelope_diameter38.8 Å
Shell Rg shell_rg16.28 Å
Envelope Rg envelope_rg11.48 Å
Shape Rg shape_rg11.18 Å
Total Rg total_rg12.68 Å
Total atoms total_atoms492
Residues n_residues68
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax40.4 Å
Rg (real space) rg_real12.58 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real1.1240e+06
I(0) uncertainty (real space) i0_real_error1.2220e+04
Rg (reciprocal space) rg_reciprocal12.58 Å
I(0) (reciprocal space) i0_reciprocal1124000.0000
Solution quality estimate total_estimate0.8930
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.4 Å
Skewness Skewness skewness0.124
Kurtosis Kurtosis kurtosis-0.312
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha133000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.986
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ctfa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.45 — ClpS-like
Superfamily Superfamily superfamilyd.45.1 — ClpS-like
Family Family familyd.45.1.1 — Ribosomal protein L7/12, C-terminal domain

CATH v4.4 (1 domains)

Domain ID domain_id1ctfA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1390 — Ribosomal Protein L30; Chain: A,
Homologous superfamily homologous superfamily10 — Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS
▶

8. Citations (4)

▶

9. Files and Curves (10)