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8f6c

E. coli cytochrome bo3 ubiquinol oxidase dimer

Method: ELECTRON MICROSCOPY Dmax: 128.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome bo(3) ubiquinol oxidase subunit 1

Escherichia coli

UniProt P0ABI8

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–658 Chain E； UniProt 1–658 Not recorded Cytochrome bo(3) ubiquinol oxidase subunit 2 × 2 （P0ABJ1） Cytochrome bo(3) ubiquinol oxidase subunit 3 × 2 （P0ABJ3） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 2 （P0ABJ6） 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

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 8F6C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1FFT The structure of ubiquinol oxidase from Escherichia coli Deposited 2000-07-26 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 × 4 PDB declaration: tetrameric
Chain A 1–663（663 aa）
Not recorded 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
1FFT The structure of ubiquinol oxidase from Escherichia coli Deposited 2000-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–663（663 aa）
Not recorded 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
7CUB 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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
8QQK Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs Deposited 2023-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 9 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 1–658； UniProt 1–658 Author chain E； PDBConstruct 1–658； UniProt 1–658

Cytochrome bo(3) ubiquinol oxidase subunit 2

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain B； UniProt 24–283 Chain F； UniProt 24–283 Not recorded Cytochrome bo(3) ubiquinol oxidase subunit 1 × 2 （P0ABI8） Cytochrome bo(3) ubiquinol oxidase subunit 3 × 2 （P0ABJ3） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 2 （P0ABJ6） 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

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 8F6C 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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
1FFT The structure of ubiquinol oxidase from Escherichia coli Deposited 2000-07-26 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 × 4 PDB declaration: tetrameric
Chain B 1–315（315 aa）
Not recorded 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
1FFT The structure of ubiquinol oxidase from Escherichia coli Deposited 2000-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–315（315 aa）
Not recorded 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
7CUB 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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
8GO3 Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent Deposited 2022-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 11 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 1–260； UniProt 24–283 Author chain F； PDBConstruct 1–260； UniProt 24–283

Cytochrome bo(3) ubiquinol oxidase subunit 3

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain C； UniProt 21–204 Chain G； UniProt 21–204 Not recorded Cytochrome bo(3) ubiquinol oxidase subunit 1 × 2 （P0ABI8） Cytochrome bo(3) ubiquinol oxidase subunit 2 × 2 （P0ABJ1） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 2 （P0ABJ6） 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

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 8F6C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1FFT The structure of ubiquinol oxidase from Escherichia coli Deposited 2000-07-26 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 × 4 PDB declaration: tetrameric
Chain C 25–204（180 aa）
Not recorded 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
1FFT The structure of ubiquinol oxidase from Escherichia coli Deposited 2000-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 25–204（180 aa）
Not recorded 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
7CUB 2.55-Angstrom Cryo-EM structure of Cytochrome bo3 from Escherichia coli in Native Membrane Deposited 2020-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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
8QQK Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs Deposited 2023-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 9 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 1–184； UniProt 21–204 Author chain G； PDBConstruct 1–184； UniProt 21–204

Cytochrome bo(3) ubiquinol oxidase subunit 4

Escherichia coli

UniProt P0ABJ6

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain D； UniProt 14–109 Chain H； UniProt 14–109 Not recorded Cytochrome bo(3) ubiquinol oxidase subunit 1 × 2 （P0ABI8） Cytochrome bo(3) ubiquinol oxidase subunit 2 × 2 （P0ABJ1） Cytochrome bo(3) ubiquinol oxidase subunit 3 × 2 （P0ABJ3） 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

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 8F6C 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 mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–109（109 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 mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–109（109 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 mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–109（109 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–109（109 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–109（109 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 mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 13–108（96 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
8QQK Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs Deposited 2023-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–109（109 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

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

View Construct and Data Evidence
UniProt name CYOD_ECOLI
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–96； UniProt 14–109 Author chain H； PDBConstruct 1–96； UniProt 14–109

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 8f6c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8f6c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8f6c
Deposition date deposition_date2022-11-16
Structure title titleE. coli cytochrome bo3 ubiquinol oxidase dimer
Keywords keywords;heme-copper oxidase, proton translocation, E. coli aerobic respiratory chain, membrane protein, PROTON TRANSPORT, Structural Genomics, Center for Structural Biology of Infectious Diseases, CSBID ;; PROTON TRANSPORT
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier42.00 Å
Radius of gyration Rg (electron density) rg_electron40.89 Å
Forward intensity I(0) i0877099000.00
Molecular weight molecular_weight274130.0 kDa
Excluded volume excluded_volume354240 ų
Envelope volume envelope_volume438190 ų
Hydration-shell volume shell_volume83445 ų
Envelope diameter envelope_diameter133.9 Å
Shell Rg shell_rg50.67 Å
Envelope Rg envelope_rg40.63 Å
Shape Rg shape_rg40.91 Å
Total Rg total_rg41.30 Å
Total atoms total_atoms19344
Residues n_residues2396
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 dmax128.2 Å
Rg (real space) rg_real41.76 Å
Rg uncertainty (real space) rg_real_error0.53 Å
I(0) (real space) i0_real8.7710e+08
I(0) uncertainty (real space) i0_real_error1.3300e+07
Rg (reciprocal space) rg_reciprocal42.00 Å
I(0) (reciprocal space) i0_reciprocal877300000.0000
Solution quality estimate total_estimate0.8952
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary57.4 Å
Skewness Skewness skewness0.076
Kurtosis Kurtosis kurtosis-0.539
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha241300000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.858
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id8f6cB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily90 —
Domain ID domain_id8f6cB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id8f6cF01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily90 —
Domain ID domain_id8f6cF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
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8. Citations (1)

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9. Files and Curves (10)