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1s62

Solution structure of the Escherichia coli TolA C-terminal domain

Method: SOLUTION NMR Dmax: 58.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TolA protein

Escherichia coli

UniProt P19934

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 325–421 Fragment：C-terminal domain (residues 325-421) No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；300 K；Ionic strength (raw mmCIF value) 100mN NaCl, 50mM NaPO4；Pressure ambient NMR measurement conditions：pH 6.8；300 K；Ionic strength (raw mmCIF value) 50mN NaCl, 50mM NaPO4；Pressure ambient NMR measurement conditions：pH 6.8；300 K；Ionic strength (raw mmCIF value) 500mN NaCl, 50mM NaPO4；Pressure ambient NMR sample composition：1.4mM U-15N, 100mN NaCl, 50mM NaPO4, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：0.5mM U-15N,13C, 50mN NaCl, 50mM NaPO4, Complete protease inhibitor (Boehringer), 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：0.7mM U-15N, 500mN NaCl, 50mM NaPO4, 90% H2O, 10% D2O | 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 1S62 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1TOL FUSION OF N-TERMINAL DOMAIN OF THE MINOR COAT PROTEIN FROM GENE III IN PHAGE M13, AND C-TERMINAL DOMAIN OF E. COLI PROTEIN-TOLA Deposited 1999-05-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 295–421（127 aa） Fragment：N-TERMINAL DOMAIN OF MINOR COAT PROTEIN AND C-TERMINAL DOMAIN OF TOLA
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN AT CONCENTRATION 8-12 MG/ML IN 50 MM HEPES (PH=7.5) WITH ADDITION OF DTT C=2MM, WAS CRYSTALLIZED USING VAPOR DIFFUSION FROM THE SITTING OR HANGING DROP, WITH THE SOLUTION CONTAINING 25% PEG4000, 0.08M TRIS (PH=8.5), AND 0.15 M SODIUM ACETATE AS A PRECIPITANT. BEFORE SETTING THE DROPS, PROTEIN SOLUTION WAS MIXED WITH THE PRECIPITANT IN THE RATIO 1:1. CRYSTALS WERE GROWING BEST AT TEMPERATURE 15 DEGREES CELSIUS.
Resolution 1.85 Å R-free 0.293
3QDP Structural characterization of the interaction of colicin A, colicin N, and TolB with TolAIII translocon Deposited 2011-01-19 Different construct Different mutation/modification 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 302–421（120 aa） Fragment：TolA domain III, residues 302-421
Non-standard monomer：Yes (specific site not provided by mmCIF) NO3 NITRATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.28；293 K；0.2 M NaNO3, 2.2 M ammonium sulphate, pH 5.28, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.15 Å R-free 0.225
3QDR Structural characterization of the interaction of colicin A, colicin N, and TolB with the TolAIII translocon Deposited 2011-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 302–421（120 aa） Fragment：TolA domain III, residues 302-421
Non-standard monomer：Yes (specific site not provided by mmCIF) TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M K2HPO4, 2.2 M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.65 Å R-free 0.273
9DDM E. coli TolAQR conformation I Deposited 2024-08-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain F 2–421（420 aa）
Chain G 2–421（420 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
9DDN E. coli TolAQR conformation II Deposited 2024-08-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain F 2–421（420 aa）
Chain G 2–421（420 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–421（421 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–421（421 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 2–421（420 aa）
Chain I 2–421（420 aa）
Chain J 2–421（420 aa）
Chain K 2–421（420 aa）
Chain L 2–421（420 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 construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 2–421（420 aa）
Chain I 2–421（420 aa）
Chain J 2–421（420 aa）
Chain K 2–421（420 aa）
Chain L 2–421（420 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
9QUQ cryo-EM structure of TolQR conformation2 in SMA nanodiscs Deposited 2025-04-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–421（421 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–421（421 aa）
Chain I 1–421（421 aa）
Chain J 1–421（421 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

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOLA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–100； UniProt 325–421

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 1s62

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1s62
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1s62
Deposition date deposition_date2004-01-22
Structure title titleSolution structure of the Escherichia coli TolA C-terminal domain
Keywords keywordstol g3p interaction, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.97 Å
Radius of gyration Rg (electron density) rg_electron14.49 Å
Forward intensity I(0) i0409655000.00
Molecular weight molecular_weight171970.0 kDa
Excluded volume excluded_volume216200 ų
Envelope volume envelope_volume47745 ų
Hydration-shell volume shell_volume19972 ų
Envelope diameter envelope_diameter65.9 Å
Shell Rg shell_rg27.13 Å
Envelope Rg envelope_rg21.32 Å
Shape Rg shape_rg14.50 Å
Total Rg total_rg14.93 Å
Total atoms total_atoms24256
Residues n_residues1632
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 dmax58.2 Å
Rg (real space) rg_real15.04 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real4.0970e+08
I(0) uncertainty (real space) i0_real_error5.4080e+06
Rg (reciprocal space) rg_reciprocal15.04 Å
I(0) (reciprocal space) i0_reciprocal409700000.0000
Solution quality estimate total_estimate0.6954
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary16.2 Å
Skewness Skewness skewness0.528
Kurtosis Kurtosis kurtosis0.299
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha228400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.440; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.716; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1s62a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.212 — TolA/TonB C-terminal domain
Superfamily Superfamily superfamilyd.212.1 — TolA/TonB C-terminal domain
Family Family familyd.212.1.1 — TolA
Domain ID domain_idd1s62a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1s62a4
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1s62A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1150 — Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)