6wti

The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli

Method: ELECTRON MICROSCOPY Dmax: 102.4 Å Quality: EXCELLENT

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

Cytochrome o ubiquinol oxidase, subunit I

Escherichia coli

UniProt H4KCU1

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 o ubiquinol oxidase × 1 (D6I7E4) Cytochrome o ubiquinol oxidase, subunit IV × 1 (I2RK84) 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

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H4KCU1_ECOLX
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 o ubiquinol oxidase, subunit I × 1 (H4KCU1) Cytochrome o ubiquinol oxidase × 1 (D6I7E4) Cytochrome o ubiquinol oxidase, subunit IV × 1 (I2RK84) 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

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.

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 o ubiquinol oxidase

Escherichia coli

UniProt D6I7E4

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 o ubiquinol oxidase, subunit I × 1 (H4KCU1) Ubiquinol oxidase subunit 2 × 1 (A0A024L5V9) Cytochrome o ubiquinol oxidase, subunit IV × 1 (I2RK84) 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

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name D6I7E4_ECOLX
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–204; UniProt 1–204

Cytochrome o ubiquinol oxidase, subunit IV

Escherichia coli

UniProt I2RK84

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 o ubiquinol oxidase, subunit I × 1 (H4KCU1) Ubiquinol oxidase subunit 2 × 1 (A0A024L5V9) Cytochrome o ubiquinol oxidase × 1 (D6I7E4) 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

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name I2RK84_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 6wti

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6wti
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6wti
Deposition date deposition_date2020-05-02
Structure title titleThe Cryo-EM structure of the ubiquinol oxidase from Escherichia coli
Keywords keywordsubiquinol oxidase cytochrome bo3, membrane protein, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.02
Radius of gyration Rg (electron density) rg_electron31.52
Forward intensity I(0) i0241066000.00
Molecular weight molecular_weight141460.0 kDa
Excluded volume excluded_volume183740 ų
Envelope volume envelope_volume213560 ų
Hydration-shell volume shell_volume53558 ų
Envelope diameter envelope_diameter111.0
Shell Rg shell_rg40.56
Envelope Rg envelope_rg31.88
Shape Rg shape_rg31.52
Total Rg total_rg32.31
Total atoms total_atoms9980
Residues n_residues1207
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax102.4
Rg (real space) rg_real32.84
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real2.4110e+08
I(0) uncertainty (real space) i0_real_error3.5580e+06
Rg (reciprocal space) rg_reciprocal32.92
I(0) (reciprocal space) i0_reciprocal241100000.0000
Solution quality estimate total_estimate0.9005
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.5
Skewness Skewness skewness0.200
Kurtosis Kurtosis kurtosis-0.454
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha51680000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.913

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6wtib1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamilyf.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
Family Family familyf.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region
Domain ID domain_idd6wtib2
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

8. Citations (1)

9. Files and Curves (10)