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

Method: ELECTRON MICROSCOPY Dmax: 74.0 Å Quality: GOOD

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

50S ribosomal protein L11

OrganismNot specified

UniProt P29395

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 7–71 Fragment:N-terminal domain 50S ribosomal protein L7/L12 × 1 (P0A7K2) Elongation factor G × 1 (P13551) 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

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.

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL11_THEMA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–65; UniProt 7–71

50S ribosomal protein L7/L12

OrganismNot specified

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 53–120 Fragment:C-terminal domain 50S ribosomal protein L11 × 1 (P29395) Elongation factor G × 1 (P13551) 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

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.

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 2
Chains and sequence ranges Author chain B; PDBConstruct 1–68; UniProt 53–120

Elongation factor G

OrganismNot specified

UniProt P13551

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 200–257 Fragment:;A portion of G' domain' ; 50S ribosomal protein L11 × 1 (P29395) 50S ribosomal protein L7/L12 × 1 (P0A7K2) 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

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.

16 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EFG_THETH
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–58; UniProt 200–257

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 2bcw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2bcw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2bcw
Deposition date deposition_date2005-10-19
Structure title titleCoordinates 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
Keywords keywordsComponents involved in interaction between EF-G AND L7/L12 stalk base of the ribosome, RIBOSOME; RIBOSOME
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier20.10
Radius of gyration Rg (electron density) rg_electron19.97
Forward intensity I(0) i06651600.00
Molecular weight molecular_weight20649.0 kDa
Excluded volume excluded_volume25497 ų
Envelope volume envelope_volume18035 ų
Hydration-shell volume shell_volume9356 ų
Envelope diameter envelope_diameter75.8
Shell Rg shell_rg22.03
Envelope Rg envelope_rg19.30
Shape Rg shape_rg19.83
Total Rg total_rg20.22
Total atoms total_atoms
Residues n_residues
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax74.0
Rg (real space) rg_real20.27
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real6.6510e+06
I(0) uncertainty (real space) i0_real_error7.7520e+04
Rg (reciprocal space) rg_reciprocal20.24
I(0) (reciprocal space) i0_reciprocal6651000.0000
Solution quality estimate total_estimate0.8297
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.0
Skewness Skewness skewness0.563
Kurtosis Kurtosis kurtosis0.059
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha980700.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.699; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.694; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2bcwa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.47 — Ribosomal L11/L12e N-terminal domain
Superfamily Superfamily superfamilyd.47.1 — Ribosomal L11/L12e N-terminal domain
Family Family familyd.47.1.1 — Ribosomal L11/L12e N-terminal domain
Domain ID domain_idd2bcwb1
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

8. Citations (4)

9. Files and Curves (10)