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- PDB-7ate: Cytochrome c oxidase structure in P-state -

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Basic information

Entry
Database: PDB / ID: 7ate
TitleCytochrome c oxidase structure in P-state
Components(Cytochrome c oxidase subunit ...) x 4
KeywordsMEMBRANE PROTEIN / Terminal oxidase Cytochrome c oxidase aa3 oxidase
Function / homology
Function and homology information


respiratory chain complex IV / aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / : / respiratory electron transport chain / electron transport chain / copper ion binding ...respiratory chain complex IV / aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / : / respiratory electron transport chain / electron transport chain / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. ...Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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
Similarity search - Domain/homology
COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / : / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / HYDROGEN PEROXIDE / Chem-PGV / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 4 / Cytochrome c oxidase subunit 1-beta
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsKolbe, F. / Safarian, S. / Michel, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structures of intermediates suggest an alternative catalytic reaction cycle for cytochrome c oxidase.
Authors: F Kolbe / S Safarian / Ż Piórek / S Welsch / H Müller / H Michel /
Abstract: Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) ...Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) to water. Their catalytic cycle has been considered to start with the oxidized form. Subsequent electron transfers lead to the E-state, the R-state (which binds oxygen), the P-state (with an already split dioxygen bond), the F-state and the O-state again. Here, we determined structures of up to 1.9 Å resolution of these intermediates by single particle cryo-EM. Our results suggest that in the O-state the active site contains a peroxide dianion and in the P-state possibly an intact dioxygen molecule, the F-state may contain a superoxide anion. Thus, the enzyme's catalytic cycle may have to be turned by 180 degrees.
History
DepositionOct 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_validate_chiral
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1-beta
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,93213
Polymers131,3684
Non-polymers3,5649
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area22880 Å2
ΔGint-242 kcal/mol
Surface area37550 Å2
MethodPISA

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Components

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Cytochrome c oxidase subunit ... , 4 types, 4 molecules ABCD

#1: Protein Cytochrome c oxidase subunit 1-beta / Cytochrome aa3 subunit 1-beta / Cytochrome c oxidase polypeptide I-beta


Mass: 62486.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: P98002, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / Cytochrome aa3 subunit 2 / Cytochrome c oxidase polypeptide II / Oxidase aa(3) subunit 2


Mass: 32563.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: P08306, cytochrome-c oxidase
#3: Protein Cytochrome c oxidase subunit 3 / Cytochrome aa3 subunit 3 / Cytochrome c oxidase polypeptide III / Oxidase aa(3) subunit 3


Mass: 30808.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: P06030, cytochrome-c oxidase
#4: Protein/peptide Cytochrome c oxidase subunit 4 / Cytochrome aa3 subunit 4 / Cytochrome c oxidase polypeptide IV


Mass: 5509.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: P77921, cytochrome-c oxidase

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Non-polymers , 9 types, 154 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#10: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#11: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#12: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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 c oxidase with four subunits reconstituted in lipid nanodisc
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 0.127 MDa / Experimental value: NO
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Buffer solutionpH: 8
Buffer componentConc.: 50 mM / Name: Potassium Phosphate / Formula: KPi
SpecimenConc.: 2.5 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: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 4 second before plunging

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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 FIELD
Image recordingAverage exposure time: 30 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
2EPU2.8image acquisition
4CTFFIND4.1CTF correction
7UCSF Chimera1.14model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13Coot0.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268222 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 3HB3

3hb3


Accession code: 3HB3 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.019225
ELECTRON MICROSCOPYf_angle_d1.13512614
ELECTRON MICROSCOPYf_dihedral_angle_d21.2473103
ELECTRON MICROSCOPYf_chiral_restr0.0711346
ELECTRON MICROSCOPYf_plane_restr0.0071540

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