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7xmc

Cryo-EM structure of Cytochrome bo3 from Escherichia coli, apo structure with DMSO

Method: ELECTRON MICROSCOPY
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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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–663 Not recorded Ubiquinol oxidase subunit 2 × 1 （A0A024L5V9） Cytochrome bo(3) ubiquinol oxidase subunit 3 × 1 （P0ABJ3） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （P0ABJ6） 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

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 7XMC 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 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 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 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 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 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 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
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 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 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 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 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 1–663； UniProt 1–663

Ubiquinol oxidase subunit 2

Escherichia coli

UniProt A0A024L5V9

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 Cytochrome bo(3) ubiquinol oxidase subunit 1 × 1 （P0ABI8） Cytochrome bo(3) ubiquinol oxidase subunit 3 × 1 （P0ABJ3） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （P0ABJ6） 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

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 7XMC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WTI The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli Deposited 2020-05-02 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 × 9 U9V pentadecyl(tetradecyl)peroxyanhydride × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
7N9Z E. coli cytochrome bo3 in MSP nanodisc Deposited 2021-06-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–315（315 aa）
Not recorded UQ8 Ubiquinone-8 × 1 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 9 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 HEO HEME O × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CDL CARDIOLIPIN × 1 CU COPPER (II) ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.19 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 structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–315（315 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A024L5V9_ECOLX
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–315； UniProt 1–315

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–204 Not recorded Cytochrome bo(3) ubiquinol oxidase subunit 1 × 1 （P0ABI8） Ubiquinol oxidase subunit 2 × 1 （A0A024L5V9） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （P0ABJ6） 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

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 7XMC 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 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 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 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 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 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 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 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
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 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 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 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 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 1–204； UniProt 1–204

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain D； UniProt 1–109 Not recorded Cytochrome bo(3) ubiquinol oxidase subunit 1 × 1 （P0ABI8） Ubiquinol oxidase subunit 2 × 1 （A0A024L5V9） Cytochrome bo(3) ubiquinol oxidase subunit 3 × 1 （P0ABJ3） 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

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 7XMC 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 conditions 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 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 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 conditions 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
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 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 ligand/ion Different experimental conditions 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
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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 14–109（96 aa）
Chain H 14–109（96 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 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 1–109； UniProt 1–109

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

暂无 SAXS 图

P(r) Distance Distribution P(r) Distribution

暂无 P(r) 图
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7xmc
Deposition date deposition_date2022-04-25
Structure title titleCryo-EM structure of Cytochrome bo3 from Escherichia coli, apo structure with DMSO
Keywords keywordsrespiratory enzyme, membrane protein, heme protein, apo structure, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

该条目暂无 SAXS 数据。

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

该条目暂无 P(r) 分析数据。

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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8. Citations (1)

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9. Files and Curves (0)