8D4T

Mammalian CIV with GDN bound

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Bos taurus
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2022-06-02 Released: 2022-07-06 
  • Deposition Author(s): Di Trani, J., Rubinstein, J.
  • Funding Organization(s): Canadian Institutes of Health Research (CIHR), Knut and Alice Wallenberg Foundation, Swedish Research Council

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of mammalian complex IV inhibition by steroids.

Di Trani, J.M.Moe, A.Riepl, D.Saura, P.Kaila, V.R.I.Brzezinski, P.Rubinstein, J.L.

(2022) Proc Natl Acad Sci U S A 119: e2205228119-e2205228119

  • DOI: https://doi.org/10.1073/pnas.2205228119
  • Primary Citation of Related Structures:  
    8D4T

  • PubMed Abstract: 

    The mitochondrial electron transport chain maintains the proton motive force that powers adenosine triphosphate (ATP) synthesis. The energy for this process comes from oxidation of reduced nicotinamide adenine dinucleotide (NADH) and succinate, with the electrons from this oxidation passed via intermediate carriers to oxygen. Complex IV (CIV), the terminal oxidase, transfers electrons from the intermediate electron carrier cytochrome c to oxygen, contributing to the proton motive force in the process. Within CIV, protons move through the K and D pathways during turnover. The former is responsible for transferring two protons to the enzyme's catalytic site upon its reduction, where they eventually combine with oxygen and electrons to form water. CIV is the main site for respiratory regulation, and although previous studies showed that steroid binding can regulate CIV activity, little is known about how this regulation occurs. Here, we characterize the interaction between CIV and steroids using a combination of kinetic experiments, structure determination, and molecular simulations. We show that molecules with a sterol moiety, such as glyco-diosgenin and cholesteryl hemisuccinate, reversibly inhibit CIV. Flash photolysis experiments probing the rapid equilibration of electrons within CIV demonstrate that binding of these molecules inhibits proton uptake through the K pathway. Single particle cryogenic electron microscopy (cryo-EM) of CIV with glyco-diosgenin reveals a previously undescribed steroid binding site adjacent to the K pathway, and molecular simulations suggest that the steroid binding modulates the conformational dynamics of key residues and proton transfer kinetics within this pathway. The binding pose of the sterol group sheds light on possible structural gating mechanisms in the CIV catalytic cycle.


  • Organizational Affiliation

    Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada M5G 0A4.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1A [auth N]513Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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UniProt GroupP00396
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2B [auth O]227Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P68530 (Bos taurus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3C [auth P]258Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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UniProt GroupP00415
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialD [auth Q]137Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialE [auth R]102Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00426
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialF [auth S]91Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialG [auth T]72Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1H [auth U]78Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CI [auth V]70Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialJ [auth W]55Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrialK [auth X]47Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialL [auth Y]46Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8A, mitochondrial43Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P10176 (Homo sapiens)
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PHAROS:  P10176
GTEx:  ENSG00000176340 
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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Q [auth N],
R [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

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V [auth P](1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N
PGV
Query on PGV

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S [auth N],
W [auth P]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
9Z9 (Subject of Investigation/LOI)
Query on 9Z9

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X [auth P](3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
C34 H56 O5
CEEBZAXXSRFQIC-GZSGZGDASA-N
ZN
Query on ZN

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Y [auth S]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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N,
T [auth O],
U [auth O]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG
Query on MG

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O [auth N]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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P [auth N]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A [auth N]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT162186
Knut and Alice Wallenberg FoundationSweden2019.0043
Swedish Research CouncilSweden2018-04619
Swedish Research CouncilSweden016-07213

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references