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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA,
W [auth a]
457Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP07256
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Entity ID: 2
MoleculeChainsSequence 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
MoleculeChainsSequence 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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Entity ID: 4
MoleculeChainsSequence 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
MoleculeChainsSequence 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
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7, mitochondrialBA [auth f],
F
127Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence 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
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8, mitochondrialDA [auth h],
H
94Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bEA [auth j],
I [auth J]
385Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence 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
MoleculeChainsSequence 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
MoleculeChainsSequence 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
MoleculeChainsSequence 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
MoleculeChainsSequence 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
MoleculeChainsSequence 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
MoleculeChainsSequence 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
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 9, mitochondrialMA [auth r],
Q [auth R]
59Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 13, mitochondrialNA [auth s],
R [auth S]
129Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4, mitochondrialOA [auth t],
S [auth T]
155Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChainsSequence 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
MoleculeChainsSequence 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
MoleculeChainsSequence 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
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
FES
Query on FES

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

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NB [auth K],
RC [auth k]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
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