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- PDB-7n9z: E. coli cytochrome bo3 in MSP nanodisc -

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Basic information

Entry
Database: PDB / ID: 7n9z
TitleE. coli cytochrome bo3 in MSP nanodisc
Components
  • (Cytochrome o ubiquinol oxidase, subunit ...) x 2
  • Cytochrome o ubiquinol oxidase
  • Ubiquinol oxidase subunit 2
KeywordsMEMBRANE PROTEIN / Ubiquinone / Heme-copper Oxidoreductase / Electron transport / Bioenergetics / Proton pump
Function / homology
Function and homology information


cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / electron transport coupled proton transport / cytochrome-c oxidase activity / respirasome / aerobic respiration / membrane => GO:0016020 ...cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / electron transport coupled proton transport / cytochrome-c oxidase activity / respirasome / aerobic respiration / membrane => GO:0016020 / copper ion binding / heme binding / plasma membrane
Similarity search - Function
Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / COX aromatic rich motif / Prokaryotic Cytochrome C oxidase subunit IV / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain ...Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / COX aromatic rich motif / Prokaryotic Cytochrome C oxidase subunit IV / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / HEME O / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Ubiquinone-8 / Ubiquinol oxidase subunit 2 / Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome bo(3) ubiquinol oxidase subunit 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsVallese, F. / Clarke, O.B.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Cryo-EM structures of cytochrome reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.
Authors: Jiao Li / Long Han / Francesca Vallese / Ziqiao Ding / Sylvia K Choi / Sangjin Hong / Yanmei Luo / Bin Liu / Chun Kit Chan / Emad Tajkhorshid / Jiapeng Zhu / Oliver Clarke / Kai Zhang / Robert Gennis /
Abstract: Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) ...Two independent structures of the proton-pumping, respiratory cytochrome ubiquinol oxidase (cyt ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene-maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme , heme , and Cu), the redox-active cross-linked histidine-tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75 and R71 In both structures, residue H98 occupies two conformations. In conformation 1, H98 forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 has flipped to form a hydrogen bond with E14 at the N-terminal end of TM0. We propose that H98 dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98.
History
DepositionJun 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
F: Cytochrome o ubiquinol oxidase, subunit I
G: Ubiquinol oxidase subunit 2
H: Cytochrome o ubiquinol oxidase
I: Cytochrome o ubiquinol oxidase, subunit IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,83021
Polymers144,0524
Non-polymers11,77817
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Cytochrome o ubiquinol oxidase, subunit ... , 2 types, 2 molecules FI

#1: Protein Cytochrome o ubiquinol oxidase, subunit I


Mass: 74424.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: H4KCU1, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
#4: Protein Cytochrome o ubiquinol oxidase, subunit IV


Mass: 12037.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: I2RK84, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor

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Protein , 2 types, 2 molecules GH

#2: Protein Ubiquinol oxidase subunit 2 /


Mass: 34947.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A024L5V9
#3: Protein Cytochrome o ubiquinol oxidase


Mass: 22642.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D6I7E4

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Non-polymers , 9 types, 267 molecules

#5: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H74O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#7: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#8: Chemical ChemComp-HEO / HEME O / Heme O


Mass: 838.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H58FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#11: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cytochrome bo 3 ubiquinol oxidase / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Buffer component
IDConc.FormulaBuffer-ID
1150 mMNaClSodium chloride1
220 mMHEPES1
SpecimenConc.: 2.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94681 / Symmetry type: POINT
Atomic model buildingPDB-ID: 1FFT

1fft

RefinementHighest resolution: 2.19 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410526
ELECTRON MICROSCOPYf_angle_d0.64114235
ELECTRON MICROSCOPYf_dihedral_angle_d15.8271968
ELECTRON MICROSCOPYf_chiral_restr0.0421526
ELECTRON MICROSCOPYf_plane_restr0.0041657

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