1fft

The structure of ubiquinol oxidase from Escherichia coli

Method: X-RAY DIFFRACTION D_max: 236.4 Å Quality: REASONABLE

▼

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

UBIQUINOL OXIDASE

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–663	Not recorded	UBIQUINOL OXIDASE × 1 （P0ABJ1） UBIQUINOL OXIDASE × 1 （P0ABJ3） UBIQUINOL OXIDASE × 1 CU COPPER (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；9-10% PEG 1500, 100 mM NaCl, 100 mM MgCl2, 5% ethanol & 100 mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.50 Å
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 1–663	Not recorded	UBIQUINOL OXIDASE × 1 （P0ABJ1） UBIQUINOL OXIDASE × 1 （P0ABJ3） UBIQUINOL OXIDASE × 1 CU COPPER (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；9-10% PEG 1500, 100 mM NaCl, 100 mM MgCl2, 5% ethanol & 100 mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.50 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 1FFT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7CUB 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-22	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 1–663（663 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
7CUQ 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-24	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 1–663（663 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.64 Å
7CUW Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli Deposited 2020-08-25	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 1–663（663 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
7XMC Cryo-EM structure of Cytochrome bo3 from Escherichia coli, apo structure with DMSO Deposited 2022-04-25	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 1–663（663 aa）	Not recorded	HEO HEME O × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CU COPPER (II) ION × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 2 UNX UNKNOWN LIGAND × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
7XMD Cryo-EM structure of Cytochrome bo3 from Escherichia coli, the structure complexed with an allosteric inhibitor N4 Deposited 2022-04-25	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 1–663（663 aa）	Not recorded	HEO HEME O × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CU COPPER (II) ION × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 2 JYR methyl 3-oxidanyl-5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-1-benzothiophene-2-carboxylate × 1 UNX UNKNOWN LIGAND × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å
8F68 E. coli cytochrome bo3 ubiquinol oxidase monomer Deposited 2022-11-16	Different construct 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 1–658（658 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8F6C E. coli cytochrome bo3 ubiquinol oxidase dimer Deposited 2022-11-16	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 × 8 PDB declaration: octameric	Chain A 1–658（658 aa） Chain E 1–658（658 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 HEO HEME O × 2 CU COPPER (II) ION × 2 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
8QQK Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs Deposited 2023-10-05	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 1–663（663 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris-HCL, 150mM NaCl, 2% Glycerol, filtered and degassed. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

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

View Construct and Data Evidence

UniProt name	CYOB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–663； UniProt 1–663 Author chain F； PDBConstruct 1–663； UniProt 1–663

UBIQUINOL OXIDASE

Escherichia coli

UniProt P0ABJ1

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–315	Not recorded	UBIQUINOL OXIDASE × 1 （P0ABI8） UBIQUINOL OXIDASE × 1 （P0ABJ3） UBIQUINOL OXIDASE × 1 CU COPPER (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；9-10% PEG 1500, 100 mM NaCl, 100 mM MgCl2, 5% ethanol & 100 mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.50 Å
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain G； UniProt 1–315	Not recorded	UBIQUINOL OXIDASE × 1 （P0ABI8） UBIQUINOL OXIDASE × 1 （P0ABJ3） UBIQUINOL OXIDASE × 1 CU COPPER (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；9-10% PEG 1500, 100 mM NaCl, 100 mM MgCl2, 5% ethanol & 100 mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1FFT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CYW QUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II) (CYOA) Deposited 1995-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 111–315（205 aa） Fragment：PERIPLASMIC FRAGMENT (RESIDUES 111 - 315)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.326
1CYW QUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II) (CYOA) Deposited 1995-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 111–315（205 aa） Fragment：PERIPLASMIC FRAGMENT (RESIDUES 111 - 315)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.326
1CYX QUINOL OXIDASE (PERIPLASMIC FRAGMENT OF SUBUNIT II WITH ENGINEERED CU-A BINDING SITE)(CYOA) Deposited 1995-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 111–315（205 aa） Fragment：PERIPLASMIC FRAGMENT (RESIDUES 111 - 315)	Mutation：N172H, S207C, S209E, Y210I, S211C, F215H	CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.30 Å R-free 0.316
7CUB 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-22	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 25–315（291 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
7CUQ 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-24	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 25–315（291 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.64 Å
7CUW Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli Deposited 2020-08-25	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 25–315（291 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
8F68 E. coli cytochrome bo3 ubiquinol oxidase monomer Deposited 2022-11-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 24–283（260 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8F6C E. coli cytochrome bo3 ubiquinol oxidase dimer Deposited 2022-11-16	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 × 8 PDB declaration: octameric	Chain B 24–283（260 aa） Chain F 24–283（260 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 HEO HEME O × 2 CU COPPER (II) ION × 2 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
8GO3 Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent Deposited 2022-08-24	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–315（315 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 UQ8 Ubiquinone-8 × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
8QQK Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs Deposited 2023-10-05	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–315（315 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris-HCL, 150mM NaCl, 2% Glycerol, filtered and degassed. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYOA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–315； UniProt 1–315 Author chain G； PDBConstruct 1–315； UniProt 1–315

UBIQUINOL OXIDASE

Escherichia coli

UniProt P0ABJ3

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 25–204	Not recorded	UBIQUINOL OXIDASE × 1 （P0ABI8） UBIQUINOL OXIDASE × 1 （P0ABJ1） UBIQUINOL OXIDASE × 1 CU COPPER (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；9-10% PEG 1500, 100 mM NaCl, 100 mM MgCl2, 5% ethanol & 100 mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.50 Å
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain H； UniProt 25–204	Not recorded	UBIQUINOL OXIDASE × 1 （P0ABI8） UBIQUINOL OXIDASE × 1 （P0ABJ1） UBIQUINOL OXIDASE × 1 CU COPPER (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；9-10% PEG 1500, 100 mM NaCl, 100 mM MgCl2, 5% ethanol & 100 mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1FFT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7CUB 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-22	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–204（204 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
7CUQ 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-24	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–204（204 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.64 Å
7CUW Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli Deposited 2020-08-25	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–204（204 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 UQ8 Ubiquinone-8 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
7XMC Cryo-EM structure of Cytochrome bo3 from Escherichia coli, apo structure with DMSO Deposited 2022-04-25	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–204（204 aa）	Not recorded	HEO HEME O × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CU COPPER (II) ION × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 2 UNX UNKNOWN LIGAND × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
7XMD Cryo-EM structure of Cytochrome bo3 from Escherichia coli, the structure complexed with an allosteric inhibitor N4 Deposited 2022-04-25	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–204（204 aa）	Not recorded	HEO HEME O × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CU COPPER (II) ION × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 2 JYR methyl 3-oxidanyl-5-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-1-benzothiophene-2-carboxylate × 1 UNX UNKNOWN LIGAND × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å
8F68 E. coli cytochrome bo3 ubiquinol oxidase monomer Deposited 2022-11-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 21–204（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8F6C E. coli cytochrome bo3 ubiquinol oxidase dimer Deposited 2022-11-16	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 × 8 PDB declaration: octameric	Chain C 21–204（184 aa） Chain G 21–204（184 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 HEO HEME O × 2 CU COPPER (II) ION × 2 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
8QQK Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs Deposited 2023-10-05	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–204（204 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HEO HEME O × 1 CU COPPER (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris-HCL, 150mM NaCl, 2% Glycerol, filtered and degassed. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

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

View Construct and Data Evidence

UniProt name	CYOC_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 25–204； UniProt 25–204 Author chain H； PDBConstruct 25–204； UniProt 25–204

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1fft
Deposition date deposition_date	2000-07-26
Structure title title	The structure of ubiquinol oxidase from Escherichia coli
Keywords keywords	ELECTRON TRANSPORT, CYTOCHROME OXIDASE, MEMBRANE PROTEIN, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	94.65 Å
Radius of gyration Rg (electron density) rg_electron	95.95 Å
Forward intensity I(0) i0	602568000.00
Molecular weight molecular_weight	228330.0 kDa
Excluded volume excluded_volume	292200 Å³
Envelope volume envelope_volume	555170 Å³
Hydration-shell volume shell_volume	47705 Å³
Envelope diameter envelope_diameter	271.0 Å
Shell Rg shell_rg	106.10 Å
Envelope Rg envelope_rg	86.20 Å
Shape Rg shape_rg	95.95 Å
Total Rg total_rg	96.02 Å
Total atoms total_atoms	16136
Residues n_residues	2104
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

▼

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

Maximum dimension Dmax dmax	236.4 Å
Rg (real space) rg_real	95.09 Å
Rg uncertainty (real space) rg_real_error	1.53 Å
I(0) (real space) i0_real	5.9880e+08
I(0) uncertainty (real space) i0_real_error	1.2870e+07
Rg (reciprocal space) rg_reciprocal	85.34 Å
I(0) (reciprocal space) i0_reciprocal	584900000.0000
Solution quality estimate total_estimate	0.5403
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	44.3 Å
Skewness Skewness skewness	0.079
Kurtosis Kurtosis kurtosis	-1.715
Angular range angular_range	— – 0.0800 Å⁻¹
Current regularization parameter α current_alpha	0.0201
Highest regularization parameter α highest_alpha	7852000.0000
Real-space data points n_real_points	17
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.005; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	UBIQUINOL OXIDASE
Molecular weight formula_weight	74424.5 kDa
EC 编号 ec_number	1.10.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	16136

MFGKLSLDAVPFHEPIVMVTIAGIILGGLALVGLITYFGKWTYLWKEWLTSVDHKRLGIMYIIVAIVMLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIFTAHGVIMIFFVAMPFVIGLMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSEIAATFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDPQFHTMLMIAASGAVLIALGILCLVIQMYVSIRDRDQNRDLTGDPWGGRTLEWATSSPPPFYNFAVVPHVHERDAFWEMKEKGEAYKKPDHYEEIHMPKNSGAGIVIAAFSTIFGFAMIWHIWWLAIVGFAGMIITWIVKSFDEDVDYYVPVAEIEKLENQHFDEITKAGLKNGN

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	UBIQUINOL OXIDASE
Molecular weight formula_weight	34947.2 kDa
EC 编号 ec_number	1.10.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MRLRKYNKSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAWKYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPLAHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHSAHEGMEGMDMSHAESAH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	UBIQUINOL OXIDASE
Molecular weight formula_weight	22642.6 kDa
EC 编号 ec_number	1.10.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H

MATDTLTHATAHAHEHGHHDAGGTKIFGFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSITYGMAAIAMYKNNKSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFFALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYLMGAM

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	UBIQUINOL OXIDASE
Molecular weight formula_weight	9294.4 kDa
EC 编号 ec_number	1.10.3.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,I

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	HEME O
Molecular weight formula_weight	838.9 kDa
Source method src_method	syn
Copy count entity_count	2

▼

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1ffta_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.24 — Cytochrome c oxidase subunit I-like
Superfamily Superfamily superfamily	f.24.1 — Cytochrome c oxidase subunit I-like
Family Family family	f.24.1.1 — Cytochrome c oxidase subunit I-like

Domain ID domain_id	d1fftb1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d1fftb2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
Family Family family	f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region

Domain ID domain_id	d1fftc2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.25 — Cytochrome c oxidase subunit III-like
Superfamily Superfamily superfamily	f.25.1 — Cytochrome c oxidase subunit III-like
Family Family family	f.25.1.1 — Cytochrome c oxidase subunit III-like

Domain ID domain_id	d1fftc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1fftf_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.24 — Cytochrome c oxidase subunit I-like
Superfamily Superfamily superfamily	f.24.1 — Cytochrome c oxidase subunit I-like
Family Family family	f.24.1.1 — Cytochrome c oxidase subunit I-like

Domain ID domain_id	d1fftg1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d1fftg2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
Family Family family	f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region

Domain ID domain_id	d1ffth2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.25 — Cytochrome c oxidase subunit III-like
Superfamily Superfamily superfamily	f.25.1 — Cytochrome c oxidase subunit III-like
Family Family family	f.25.1.1 — Cytochrome c oxidase subunit III-like

Domain ID domain_id	d1ffth3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	1fftA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

Domain ID domain_id	1fftB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1fftB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1fftC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	80 — Cytochrome c oxidase, subunit III, four-helix bundle

Domain ID domain_id	1fftF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

Domain ID domain_id	1fftG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1fftG02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1fftH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	80 — Cytochrome c oxidase, subunit III, four-helix bundle

▶

8. Citations (2)

▶

Unit-cell length a length_a	92.100 Å
Unit-cell length b length_b	372.500 Å
Unit-cell length c length_c	232.700 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ff/1fft/1fft.fit
pddf	/app/data/pr_computation/ff/1fft/1fft.pr.out
profile	/app/data/saxs_computation/ff/1fft/1fft.dat

The structure of ubiquinol oxidase from Escherichia coli

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

UBIQUINOL OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

UBIQUINOL OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

UBIQUINOL OXIDASE

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)