SAXSdb — 9o40

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

Tol-Pal system protein TolQ

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 1–230 Chain B； UniProt 1–230 Chain C； UniProt 1–230 Chain D； UniProt 1–230 Chain E； UniProt 1–230	Not recorded	Tol-Pal system protein TolR × 2 （P0ABV6）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.92 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 9O40	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8ODT Structure of TolQR complex from E.coli Deposited 2023-03-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	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 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot force 10 Blot time 3 sec Wait time 2 sec	Resolution 4.20 Å
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 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 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 construct 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 construct 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
9QUQ cryo-EM structure of TolQR conformation2 in SMA nanodiscs Deposited 2025-04-11	Different oligomeric state 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 oligomeric state 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 1–230； UniProt 1–230 Author chain B； PDBConstruct 1–230； UniProt 1–230 Author chain C； PDBConstruct 1–230； UniProt 1–230 Author chain D； PDBConstruct 1–230； UniProt 1–230 Author chain E； PDBConstruct 1–230； UniProt 1–230

Tol-Pal system protein TolR

Escherichia coli

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 7.8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.92 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 9O40	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
8ODT Structure of TolQR complex from E.coli Deposited 2023-03-09	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 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot force 10 Blot time 3 sec Wait time 2 sec	Resolution 4.20 Å
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
9QUQ cryo-EM structure of TolQR conformation2 in SMA nanodiscs Deposited 2025-04-11	Different oligomeric state 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 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9o40
Deposition date deposition_date	2025-04-08
Structure title title	cryo-EM structure of TolQR conformation1 in SMA nanodiscs
Keywords keywords	Molecular motor Multi-pass membrane protein Accumulates at cell constriction sites., MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	35.47 Å
Radius of gyration Rg (electron density) rg_electron	34.96 Å
Forward intensity I(0) i0	225284000.00
Molecular weight molecular_weight	127070.0 kDa
Excluded volume excluded_volume	162070 Å³
Envelope volume envelope_volume	231540 Å³
Hydration-shell volume shell_volume	55124 Å³
Envelope diameter envelope_diameter	113.0 Å
Shell Rg shell_rg	42.15 Å
Envelope Rg envelope_rg	33.96 Å
Shape Rg shape_rg	34.95 Å
Total Rg total_rg	35.59 Å
Total atoms total_atoms	8967
Residues n_residues	1143
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	112.7 Å
Rg (real space) rg_real	35.36 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	2.2530e+08
I(0) uncertainty (real space) i0_real_error	3.8090e+06
Rg (reciprocal space) rg_reciprocal	35.43 Å
I(0) (reciprocal space) i0_reciprocal	225300000.0000
Solution quality estimate total_estimate	0.8948
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.6 Å
Skewness Skewness skewness	0.257
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35520000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Tol-Pal system protein TolQ
Molecular weight formula_weight	25623.7 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	8967

MTDMNILDLFLKASLLVKLIMLILIGFSIASWAIIIQRTRILNAAAREAEAFEDKFWSGIELSRLYQESQGKRDNLTGSEQIFYSGFKEFVRLHRANSHAPEAVVEGASRAMRISMNRELENLETHIPFLGTVGSISPYIGLFGTVWGIMHAFIALGAVKQATLQMVAPGIAEALIATAIGLFAAIPAVMAYNRLNQRVNKLELNYDNFMEEFTAILHRQAFTVSESNKG

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	511145
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Tol-Pal system protein TolR
Molecular weight formula_weight	15398.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G

MARARGRGRRDLKSEINIVPLLDVLLVLLLIFMATAPIITQSVEVDLPDATESQAVSSNDNPPVIVEVSGIGQYTVVVEKDRLERLPPEQVVAEVSSRFKANPKTVFLIGGAKDVPYDEIIKALNLLHSAGVKSVGLMTQPI

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	511145
宿主生物 host_organism	Escherichia coli BL21(DE3)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.920 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.92 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	629965

fit	/app/data/saxs_computation/o4/9o40/9o40.fit
pddf	/app/data/pr_computation/o4/9o40/9o40.pr.out
profile	/app/data/saxs_computation/o4/9o40/9o40.dat

cryo-EM structure of TolQR conformation1 in SMA nanodiscs

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

Tol-Pal system protein TolQ

State in the Current Structure

Other States of the Same Protein in the Database

Tol-Pal system protein TolR

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)