8E7S

III2IV2 respiratory supercomplex from Saccharomyces cerevisiae with 4 bound UQ6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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 of 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, Center for Membrane Biology, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas, USA. william.dowhan@uth.tmc.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA,
W [auth a]
457Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB,
X [auth b]
368Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialC,
Y [auth c]
215Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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UniProt GroupP08067
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10, mitochondrialD,
Z [auth d]
77Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9, mitochondrialAA [auth e],
E
66Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7, mitochondrialBA [auth f],
F
127Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialCA [auth g],
G
147Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8, mitochondrialDA [auth h],
H
94Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bEA [auth j],
I [auth J]
385Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1FA [auth k],
J [auth K]
534Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialGA [auth l],
K [auth L]
309Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8, mitochondrialHA [auth m],
L [auth M]
78Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7, mitochondrialIA [auth n],
M [auth N]
60Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3JA [auth o],
N [auth O]
269Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2KA [auth p],
O [auth P]
251Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6, mitochondrialLA [auth q],
P [auth Q]
148Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 9, mitochondrialMA [auth r],
Q [auth R]
59Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 13, mitochondrialNA [auth s],
R [auth S]
129Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4, mitochondrialOA [auth t],
S [auth T]
155Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP04037
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 12, mitochondrialPA [auth u],
T [auth U]
83Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 26, mitochondrialQA [auth v],
U [auth V]
66Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q2V2P9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialRA [auth w],
V [auth W]
153Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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BB [auth H]
DC [auth c]
FB [auth J]
HC [auth h]
IC [auth h]
BB [auth H],
DC [auth c],
FB [auth J],
HC [auth h],
IC [auth h],
KC [auth j],
OB [auth K],
RB [auth L],
SC [auth k],
WA [auth C]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

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MB [auth K],
PB [auth K],
TC [auth k],
UC [auth k]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PCF (Subject of Investigation/LOI)
Query on PCF

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CB [auth H]
CD [auth w]
VC [auth k]
XB [auth W]
ZA [auth E]
CB [auth H],
CD [auth w],
VC [auth k],
XB [auth W],
ZA [auth E],
ZB [auth a]
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
PEF (Subject of Investigation/LOI)
Query on PEF

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AB [auth E]
AC [auth a]
AD [auth w]
BC [auth a]
BD [auth w]
AB [auth E],
AC [auth a],
AD [auth w],
BC [auth a],
BD [auth w],
DB [auth J],
EC [auth c],
FC [auth c],
GC [auth e],
JB [auth J],
JC [auth j],
LB [auth J],
OC [auth j],
QC [auth j],
SA [auth A],
TA [auth A],
UA [auth A],
UB [auth V],
VB [auth W],
WB [auth W],
XA [auth C],
YA [auth C],
YB [auth a],
ZC [auth v]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
CN5
Query on CN5

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EB [auth J](5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
C26 H52 O13 P2
UKWPDXFRXMWSMQ-VWLOTQADSA-N
HEM
Query on HEM

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GB [auth J]
HB [auth J]
LC [auth j]
MC [auth j]
QB [auth L]
GB [auth J],
HB [auth J],
LC [auth j],
MC [auth j],
QB [auth L],
WC [auth l]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
UQ6 (Subject of Investigation/LOI)
Query on UQ6

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IB [auth J],
KB [auth J],
NC [auth j],
PC [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

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CC [auth c],
VA [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CUA
Query on CUA

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SB [auth P],
TB [auth P],
XC [auth p],
YC [auth p]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
CU
Query on CU

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NB [auth K],
RC [auth k]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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