8EC0 | pdb_00008ec0

III2IV respiratory supercomplex from Saccharomyces cerevisiae cardiolipin-lacking mutant


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural insights into cardiolipin replacement by phosphatidylglycerol in a cardiolipin-lacking yeast respiratory supercomplex.

Hryc, C.F.Mallampalli, V.K.P.S.Bovshik, E.I.Azinas, S.Fan, G.Serysheva, I.I.Sparagna, G.C.Baker, M.L.Mileykovskaya, E.Dowhan, W.

(2023) Nat Commun 14: 2783-2783

  • DOI: https://doi.org/10.1038/s41467-023-38441-5
  • Primary Citation Related Structures: 
    8E7S, 8EC0

  • PubMed Abstract: 

    Cardiolipin is a hallmark phospholipid of mitochondrial membranes. Despite established significance of cardiolipin in supporting respiratory supercomplex organization, a mechanistic understanding of this lipid-protein interaction is still lacking. To address the essential role of cardiolipin in supercomplex organization, we report cryo-EM structures of a wild type supercomplex (IV 1 III 2 IV 1 ) and a supercomplex (III 2 IV 1 ) isolated from a cardiolipin-lacking Saccharomyces cerevisiae mutant at 3.2-Å and 3.3-Å resolution, respectively, and demonstrate that phosphatidylglycerol in III 2 IV 1 occupies similar positions as cardiolipin in IV 1 III 2 IV 1 . Lipid-protein interactions within these complexes differ, which conceivably underlies the reduced level of IV 1 III 2 IV 1 and high levels of III 2 IV 1 and free III 2 and IV in mutant mitochondria. Here we show that anionic phospholipids interact with positive amino acids and appear to nucleate a phospholipid domain at the interface between the individual complexes, which dampen charge repulsion and further stabilize interaction, respectively, between individual complexes.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas, USA.

Macromolecule Content 

  • Total Structure Weight: 735.12 kDa 
  • Atom Count: 46,624 
  • Modeled Residue Count: 5,688 
  • Deposited Residue Count: 6,321 
  • Unique protein chains: 21

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA,
V [auth a]
457Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB,
W [auth b]
368Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialC,
X [auth c]
215Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9, mitochondrialD [auth E],
Y [auth e]
66Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7, mitochondrialE [auth F],
Z [auth f]
127Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialAA [auth g],
F [auth G]
147Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8, mitochondrialBA [auth h],
G [auth H]
94Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bCA [auth j],
H [auth J]
385Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1I [auth K]534Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialDA [auth l],
J [auth L]
309Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8, mitochondrialK [auth M]78Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7, mitochondrialL [auth N]60Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3M [auth O]269Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2N [auth P]251Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6, mitochondrialO [auth Q]148Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00427 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 9, mitochondrialP [auth R]59Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 13, mitochondrialQ [auth S]129Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32799 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4, mitochondrialR [auth T]155Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P04037 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 12, mitochondrialS [auth U]83Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 26, mitochondrialT [auth V]66Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q2V2P9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialU [auth W]153Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA

Query on HEA



Download:Ideal Coordinates CCD File
UA [auth K],
VA [auth K]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PGT
(Subject of Investigation/LOI)

Query on PGT



Download:Ideal Coordinates CCD File
CB [auth W]
FA [auth A]
GB [auth a]
HA [auth C]
LA [auth H]
CB [auth W],
FA [auth A],
GB [auth a],
HA [auth C],
LA [auth H],
RB [auth j],
XA [auth L]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
PCF
(Subject of Investigation/LOI)

Query on PCF



Download:Ideal Coordinates CCD File
DB [auth W],
EB [auth W],
IB [auth c],
JA [auth E]
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
PEF
(Subject of Investigation/LOI)

Query on PEF



Download:Ideal Coordinates CCD File
AB [auth V]
BB [auth V]
EA [auth A]
FB [auth a]
IA [auth C]
AB [auth V],
BB [auth V],
EA [auth A],
FB [auth a],
IA [auth C],
JB [auth c],
KA [auth H],
KB [auth j],
LB [auth j],
MA [auth J],
NA [auth J],
PB [auth j],
QB [auth j],
RA [auth J],
SA [auth J]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
MB [auth j]
NB [auth j]
OA [auth J]
PA [auth J]
SB [auth l]
MB [auth j],
NB [auth j],
OA [auth J],
PA [auth J],
SB [auth l],
WA [auth L]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
UQ6
(Subject of Investigation/LOI)

Query on UQ6



Download:Ideal Coordinates CCD File
OB [auth j],
QA [auth J]
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
C39 H60 O4
DYOSCPIQEYRQEO-XQCASOQKSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
GA [auth C],
HB [auth c]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CUA

Query on CUA



Download:Ideal Coordinates CCD File
YA [auth P],
ZA [auth P]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
TA [auth K]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM115969
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01GM063210

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary