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8go3

Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent

Method: ELECTRON MICROSCOPY Dmax: 102.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome bo(3) ubiquinol oxidase subunit 1

OrganismNot specified

UniProt B7MD89

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 Cytochrome bo(3) ubiquinol oxidase subunit 2 × 1 （P0ABJ1） ubiquinol oxidase × 1 （B6HZN6） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （C3TLX2） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name B7MD89_ECO45
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–663； UniProt 1–663

Cytochrome bo(3) ubiquinol oxidase subunit 2

OrganismNot specified

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 Cytochrome bo(3) ubiquinol oxidase subunit 1 × 1 （B7MD89） ubiquinol oxidase × 1 （B6HZN6） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （C3TLX2） 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

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 8GO3 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 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 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 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 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 ligand/ion 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 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 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 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 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
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 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 1–315； UniProt 1–315

ubiquinol oxidase

OrganismNot specified

UniProt B6HZN6

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 （B7MD89） Cytochrome bo(3) ubiquinol oxidase subunit 2 × 1 （P0ABJ1） Cytochrome bo(3) ubiquinol oxidase subunit 4 × 1 （C3TLX2） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name B6HZN6_ECOSE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–204； UniProt 1–204

Cytochrome bo(3) ubiquinol oxidase subunit 4

OrganismNot specified

UniProt C3TLX2

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 （B7MD89） Cytochrome bo(3) ubiquinol oxidase subunit 2 × 1 （P0ABJ1） ubiquinol oxidase × 1 （B6HZN6） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name C3TLX2_ECOLX
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

SAXS profile for 8go3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8go3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8go3
Deposition date deposition_date2022-08-24
最后修订 last_revision2023-08-30
Structure title titleCryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent
Keywords keywordsCytochrome bo3, ubiquinol oxidase, DDM detergent, TRANSLOCASE; TRANSLOCASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.42 Å
Radius of gyration Rg (electron density) rg_electron31.05 Å
Forward intensity I(0) i0235601000.00
Molecular weight molecular_weight138000.0 kDa
Excluded volume excluded_volume178500 ų
Envelope volume envelope_volume204280 ų
Hydration-shell volume shell_volume51993 ų
Envelope diameter envelope_diameter108.1 Å
Shell Rg shell_rg40.14 Å
Envelope Rg envelope_rg31.45 Å
Shape Rg shape_rg31.05 Å
Total Rg total_rg31.82 Å
Total atoms total_atoms9739
Residues n_residues1203
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 dmax102.1 Å
Rg (real space) rg_real32.25 Å
Rg uncertainty (real space) rg_real_error0.61 Å
I(0) (real space) i0_real2.3560e+08
I(0) uncertainty (real space) i0_real_error3.2130e+06
Rg (reciprocal space) rg_reciprocal32.32 Å
I(0) (reciprocal space) i0_reciprocal235600000.0000
Solution quality estimate total_estimate0.8240
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.6 Å
Skewness Skewness skewness0.206
Kurtosis Kurtosis kurtosis-0.442
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha50170000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000
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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 (10)