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1tqq

Structure of TolC in complex with hexamminecobalt

Method: X-RAY DIFFRACTION Dmax: 150.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Outer membrane protein tolC

Escherichia coli

UniProt P02930

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 25–495 Chain B； UniProt 25–495 Chain C； UniProt 25–495 Not recorded NCO COBALT HEXAMMINE(III) × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；0.6% detergent mixture of n-dodecyl-beta-D glucopyranoside, n-hexyl-beta-D glucopyranoside, n-heptyl-beta-D glucopyranoside and n-octyl-beta-D glucopyranoside, 1.5% 1,2,3-heptanetriol, 7% polyethylene glycol 2000 monomethyl ether, 10% polyethylene glycol 400, 10mM NaCl, 20mM MgCl2, 20mM Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.75 Å R-free 0.305

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 1TQQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EK9 2.1A X-RAY STRUCTURE OF TOLC: AN INTEGRAL OUTER MEMBRANE PROTEIN AND EFFLUX PUMP COMPONENT FROM ESCHERICHIA COLI Deposited 2000-03-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 25–452（428 aa）
Chain B 25–452（428 aa）
Chain C 25–452（428 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 2000 MME, PEG 400, Sodium Chloride, Magnesium Chloride, dodecyl glucopyrsanoside, hexyl glucopyranoside, heptyl gluocopyranoside, octyl glucopyranoside, 1,2,3-heptanetriol, Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.257
2VDD Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps Deposited 2007-10-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–450（450 aa） Fragment：RESIDUES 1-450
Chain B 1–450（450 aa） Fragment：RESIDUES 1-450
Chain C 1–450（450 aa） Fragment：RESIDUES 1-450
Mutation：YES Mutation：YES Mutation：YES CL CHLORIDE ION × 3 K POTASSIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLISED FROM 0.1M HEPES 7.5, 5% ISOPROPANOL, 10% PEG4000
Resolution 3.30 Å R-free 0.295
2VDE Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps Deposited 2007-10-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–450（450 aa） Fragment：RESIDUES 1-450
Chain B 1–450（450 aa） Fragment：RESIDUES 1-450
Chain C 1–450（450 aa） Fragment：RESIDUES 1-450
Mutation：YES Mutation：YES Mutation：YES CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 10.5；PROTEIN WAS CRYSTALLIZED FROM 0.1M CAPS PH10.5, 30% PEG400
Resolution 3.20 Å R-free 0.315
2WMZ Structure of a mutated TolC Deposited 2009-07-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–450（428 aa） Fragment：MATURE PROTEIN WITH 43 C-TERMINAL RESIDUES REMOVED, RESIDUES 23-450
Chain B 23–450（428 aa） Fragment：MATURE PROTEIN WITH 43 C-TERMINAL RESIDUES REMOVED, RESIDUES 23-450
Chain C 23–450（428 aa） Fragment：MATURE PROTEIN WITH 43 C-TERMINAL RESIDUES REMOVED, RESIDUES 23-450
Mutation：YES Mutation：YES Mutation：YES CL CHLORIDE ION × 3 PGE TRIETHYLENE GLYCOL × 5 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；50 MM TRIS PH 8.2, 50 MM NACL, 14% PEG2000, 0.075% N-DODECYL-BETA-D-MALTOSIDE, 0.3% N-OCTYL BETA-D-GLUCOPYRANOSIDE
Resolution 2.90 Å R-free 0.301
2XMN High resolution snapshots of defined TolC open states present an iris- like movement of periplasmic entrance helices Deposited 2010-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–450（428 aa） Fragment：RESIDUES 23-450
Chain B 23–450（428 aa） Fragment：RESIDUES 23-450
Chain C 23–450（428 aa） Fragment：RESIDUES 23-450
Mutation：YES Mutation：YES Mutation：YES CL CHLORIDE ION × 3 LMT DODECYL-BETA-D-MALTOSIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；PH 7.4
Resolution 2.85 Å R-free 0.309
5NG5 multi-drug efflux; membrane transport; RND superfamily; Drug resistance Deposited 2017-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain C 1–493（493 aa）
Chain F 1–493（493 aa）
Chain I 1–493（493 aa）
Not recorded 5QF 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；a 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh)
Resolution 6.50 Å
5NIK Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump Deposited 2017-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain A 23–493（471 aa）
Chain B 23–493（471 aa）
Chain C 23–493（471 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
5NIL Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump-MacB section Deposited 2017-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain A 23–493（471 aa）
Chain B 23–493（471 aa）
Chain C 23–493（471 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
5O66 Asymmetric AcrABZ-TolC Deposited 2017-06-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain A 1–493（493 aa）
Chain B 1–493（493 aa）
Chain C 1–493（493 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
5V5S multi-drug efflux; membrane transport; RND superfamily; Drug resistance Deposited 2017-03-15 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 × 12 PDB declaration: dodecameric
Chain A 23–464（442 aa）
Chain B 23–464（442 aa）
Chain C 23–464（442 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；a 3ul aliquot at a concentration of 2 mg per ml was applied onto glow-discharged holey carbon grid (Quantifoil Au R1.21.3, 300 mesh)
Resolution 6.50 Å
6WXH Colicin E1 fragment in nanodisc-embedded TolC Deposited 2020-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–493（493 aa）
Chain B 1–493（493 aa）
Chain C 1–493（493 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
6WXI Colicin E1 fragment in nanodisc-embedded TolC Deposited 2020-05-10 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–493（493 aa）
Chain B 1–493（493 aa）
Chain C 1–493（493 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.84 Å
8ZAL EmrAB-TolC MFS-type tripartite multidrug efflux pump EA Deposited 2024-04-25 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 × 10 PDB declaration: decameric
Chain G 23–450（428 aa）
Chain H 23–450（428 aa）
Chain I 23–450（428 aa）
Mutation：V169L Mutation：V169L Mutation：V169L No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8ZAR EmrAB-TolC MFS-type tripartite multidrug efflux pump FA Deposited 2024-04-25 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 × 10 PDB declaration: decameric
Chain G 1–493（493 aa）
Chain H 1–493（493 aa）
Chain I 1–493（493 aa）
Mutation：V191L Mutation：V191L Mutation：V191L No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9QGY Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump Deposited 2025-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain A 23–493（471 aa）
Chain B 23–493（471 aa）
Chain C 23–493（471 aa）
Not recorded CL CHLORIDE ION × 3 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
9TG4 Structure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump Deposited 2025-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric
Chain A 23–493（471 aa）
Chain B 23–493（471 aa）
Chain C 23–493（471 aa）
Not recorded CL CHLORIDE ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
9V52 Structure of TolC and YbjP closed state complex Deposited 2025-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C1 1–493（493 aa）
Chain C2 1–493（493 aa）
Chain C3 1–493（493 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.56 Å
9V53 Structure of TolC, YbjP, and AcrABZ complex Deposited 2025-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain C1 1–493（493 aa）
Chain C2 1–493（493 aa）
Chain C3 1–493（493 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.39 Å
9V55 Structure of TolC, YbjP, and AcrA complex Deposited 2025-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C1 1–493（493 aa）
Chain C2 1–493（493 aa）
Chain C3 1–493（493 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.26 Å

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOLC_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–471； UniProt 25–495 Author chain B； PDBConstruct 1–471； UniProt 25–495 Author chain C； PDBConstruct 1–471； UniProt 25–495

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 1tqq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1tqq
Deposition date deposition_date2004-06-18
Structure title titleStructure of TolC in complex with hexamminecobalt
Keywords keywordsBeta-barrel, alpha-barrel, transport protein; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.14 Å
Radius of gyration Rg (electron density) rg_electron41.06 Å
Forward intensity I(0) i0330329000.00
Molecular weight molecular_weight140990.0 kDa
Excluded volume excluded_volume174300 ų
Envelope volume envelope_volume264330 ų
Hydration-shell volume shell_volume58150 ų
Envelope diameter envelope_diameter149.3 Å
Shell Rg shell_rg43.03 Å
Envelope Rg envelope_rg40.23 Å
Shape Rg shape_rg41.06 Å
Total Rg total_rg41.18 Å
Total atoms total_atoms9922
Residues n_residues1284
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 dmax150.1 Å
Rg (real space) rg_real41.49 Å
Rg uncertainty (real space) rg_real_error2.01 Å
I(0) (real space) i0_real3.3030e+08
I(0) uncertainty (real space) i0_real_error6.6460e+06
Rg (reciprocal space) rg_reciprocal41.15 Å
I(0) (reciprocal space) i0_reciprocal330200000.0000
Solution quality estimate total_estimate0.7816
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.5 Å
Skewness Skewness skewness0.682
Kurtosis Kurtosis kurtosis0.104
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35210000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.470; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.782
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1tqqa_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.5 — Outer membrane efflux proteins (OEP)
Superfamily Superfamily superfamilyf.5.1 — Outer membrane efflux proteins (OEP)
Family Family familyf.5.1.1 — Outer membrane efflux proteins (OEP)
Domain ID domain_idd1tqqb_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.5 — Outer membrane efflux proteins (OEP)
Superfamily Superfamily superfamilyf.5.1 — Outer membrane efflux proteins (OEP)
Family Family familyf.5.1.1 — Outer membrane efflux proteins (OEP)
Domain ID domain_idd1tqqc_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.5 — Outer membrane efflux proteins (OEP)
Superfamily Superfamily superfamilyf.5.1 — Outer membrane efflux proteins (OEP)
Family Family familyf.5.1.1 — Outer membrane efflux proteins (OEP)

CATH v4.4 (3 domains)

Domain ID domain_id1tqqA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1600 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily10 — Outer membrane efflux proteins (OEP)
Domain ID domain_id1tqqB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1600 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily10 — Outer membrane efflux proteins (OEP)
Domain ID domain_id1tqqC00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1600 — Outer membrane efflux proteins (OEP)
Homologous superfamily homologous superfamily10 — Outer membrane efflux proteins (OEP)
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8. Citations (1)

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9. Files and Curves (10)