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8odt

Structure of TolQR complex from E.coli

Method: ELECTRON MICROSCOPY Dmax: 113.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tol-Pal system protein TolQ

Escherichia coli K-12

UniProt P0ABU9

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain A； UniProt 2–230 Chain B； UniProt 2–230 Chain C； UniProt 2–230 Chain D； UniProt 2–230 Chain E； UniProt 2–230 Not recorded Tol-Pal system protein TolR × 2 （P0ABV6） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；Blot force 10 Blot time 3 sec Wait time 2 sec Resolution 4.20 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.

Other PDB Difference from Current Entry 8ODT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9K49 Cryo-EM structure of inner membrane TolQRA complex in CYMAL-6-Neopentyl Glycol detergent micelles Deposited 2024-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–230（230 aa）
Chain B 1–230（230 aa）
Chain C 1–230（230 aa）
Chain D 1–230（230 aa）
Chain E 1–230（230 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Phosphate-buffered saline (PBS) buffer at pH 7.5 (20 mM PBS pH 7.5, 300 mM NaCl) with 20 mM Imidazole and 0.04 mM CYMAL-6 Neopentyl Glycol detergent
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9KCH Cryo-EM structure of inner membrane TolQRA complex in CYMAL-6-Neopentyl Glycol detergent micelles Deposited 2024-11-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–230（230 aa）
Chain B 1–230（230 aa）
Chain C 1–230（230 aa）
Chain D 1–230（230 aa）
Chain E 1–230（230 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Phosphate-buffered saline (PBS) buffer at pH 7.5 (20 mM PBS pH 7.5, 300 mM NaCl) with 20 mM Imidazole and 0.04 mM CYMAL-6 Neopentyl Glycol detergent
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.19 Å
9KPZ Structure of TolQRA complex at pH 5.4 from E.coli Deposited 2024-11-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 2–230（229 aa）
Chain B 2–230（229 aa）
Chain C 2–230（229 aa）
Chain D 2–230（229 aa）
Chain E 2–230（229 aa）
Not recorded 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 5.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
9KQ0 Structure of TolQRA complex at pH 8.0 from E.coli Deposited 2024-11-24 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 2–230（229 aa）
Chain B 2–230（229 aa）
Chain C 2–230（229 aa）
Chain D 2–230（229 aa）
Chain E 2–230（229 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9O40 cryo-EM structure of TolQR conformation1 in SMA nanodiscs Deposited 2025-04-08 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–230（230 aa）
Chain B 1–230（230 aa）
Chain C 1–230（230 aa）
Chain D 1–230（230 aa）
Chain E 1–230（230 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
9QUQ cryo-EM structure of TolQR conformation2 in SMA nanodiscs Deposited 2025-04-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–230（230 aa）
Chain B 1–230（230 aa）
Chain C 1–230（230 aa）
Chain D 1–230（230 aa）
Chain E 1–230（230 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9QVD cryo-EM structure of TolQRA in nanodiscs Deposited 2025-04-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–230（230 aa）
Chain B 1–230（230 aa）
Chain C 1–230（230 aa）
Chain D 1–230（230 aa）
Chain E 1–230（230 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOLQ_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–230； UniProt 2–230 Author chain B； PDBConstruct 2–230； UniProt 2–230 Author chain C； PDBConstruct 2–230； UniProt 2–230 Author chain D； PDBConstruct 2–230； UniProt 2–230 Author chain E； PDBConstruct 2–230； UniProt 2–230

Tol-Pal system protein TolR

Escherichia coli K-12

UniProt P0ABV6

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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count Chain F； UniProt 1–142 Chain G； UniProt 1–142 Not recorded Tol-Pal system protein TolQ × 5 （P0ABU9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；Blot force 10 Blot time 3 sec Wait time 2 sec Resolution 4.20 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.

Other PDB Difference from Current Entry 8ODT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5BY4 Structure and function of the Escherichia coli Tol-Pal stator protein TolR Deposited 2015-06-10 Different construct Different mutation/modification Different oligomeric state 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 36–142（107 aa） Fragment：UNP RESIDUES 36-142
Not recorded NA SODIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Hepes buffer pH 7.5, 1.0 M sodium phosphate and 0.8 M potassium phosphate
Resolution 1.70 Å R-free 0.215
9K49 Cryo-EM structure of inner membrane TolQRA complex in CYMAL-6-Neopentyl Glycol detergent micelles Deposited 2024-10-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–142（142 aa）
Chain G 1–142（142 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Phosphate-buffered saline (PBS) buffer at pH 7.5 (20 mM PBS pH 7.5, 300 mM NaCl) with 20 mM Imidazole and 0.04 mM CYMAL-6 Neopentyl Glycol detergent
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9KCH Cryo-EM structure of inner membrane TolQRA complex in CYMAL-6-Neopentyl Glycol detergent micelles Deposited 2024-11-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–142（142 aa）
Chain G 1–142（142 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Phosphate-buffered saline (PBS) buffer at pH 7.5 (20 mM PBS pH 7.5, 300 mM NaCl) with 20 mM Imidazole and 0.04 mM CYMAL-6 Neopentyl Glycol detergent
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.19 Å
9KPZ Structure of TolQRA complex at pH 5.4 from E.coli Deposited 2024-11-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–142（142 aa）
Chain G 1–142（142 aa）
Not recorded 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 5.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
9KQ0 Structure of TolQRA complex at pH 8.0 from E.coli Deposited 2024-11-24 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–142（142 aa）
Chain G 1–142（142 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9O40 cryo-EM structure of TolQR conformation1 in SMA nanodiscs Deposited 2025-04-08 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–142（142 aa）
Chain G 1–142（142 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
9QUQ cryo-EM structure of TolQR conformation2 in SMA nanodiscs Deposited 2025-04-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–142（142 aa）
Chain G 1–142（142 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9QVD cryo-EM structure of TolQRA in nanodiscs Deposited 2025-04-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain F 1–142（142 aa）
Chain G 1–142（142 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOLR_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain F； PDBConstruct 1–142； UniProt 1–142 Author chain G； PDBConstruct 1–142； UniProt 1–142

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 8odt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8odt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8odt
Deposition date deposition_date2023-03-09
Structure title titleStructure of TolQR complex from E.coli
Keywords keywordsTolQ, TolR, Tol-Pal, complex, inner membrane, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.68 Å
Radius of gyration Rg (electron density) rg_electron34.97 Å
Forward intensity I(0) i0247775000.00
Molecular weight molecular_weight132100.0 kDa
Excluded volume excluded_volume167840 ų
Envelope volume envelope_volume227310 ų
Hydration-shell volume shell_volume54113 ų
Envelope diameter envelope_diameter119.9 Å
Shell Rg shell_rg41.94 Å
Envelope Rg envelope_rg34.15 Å
Shape Rg shape_rg34.93 Å
Total Rg total_rg35.66 Å
Total atoms total_atoms18800
Residues n_residues1188
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax113.4 Å
Rg (real space) rg_real35.58 Å
Rg uncertainty (real space) rg_real_error1.01 Å
I(0) (real space) i0_real2.4780e+08
I(0) uncertainty (real space) i0_real_error4.2170e+06
Rg (reciprocal space) rg_reciprocal35.64 Å
I(0) (reciprocal space) i0_reciprocal247800000.0000
Solution quality estimate total_estimate0.8927
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.8 Å
Skewness Skewness skewness0.272
Kurtosis Kurtosis kurtosis-0.391
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28300000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.918
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)