6GIQ

Saccharomyces cerevisiae respiratory supercomplex III2IV


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Cryo-EM structure of the yeast respiratory supercomplex.

Rathore, S.Berndtsson, J.Marin-Buera, L.Conrad, J.Carroni, M.Brzezinski, P.Ott, M.

(2019) Nat. Struct. Mol. Biol. 26: 50-57

  • DOI: 10.1038/s41594-018-0169-7

  • PubMed Abstract: 
  • Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory s ...

    Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes III 2 IV and III 2 IV 2 , at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. martin.ott@dbb.su.se.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 1, mitochondrial
A, L
457Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COR1 (QCR1)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07256
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 2, mitochondrial
B, M
368Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR2 (COR2, UCR2)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07257
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C, N
385Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COB (CYTB)
EC: 7.1.1.8
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00163
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein, mitochondrial
D, O
309Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CYT1 (CTC1)
EC: 7.1.1.8
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07143
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
E, P
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RIP1
EC: 7.1.1.8
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08067
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 6
F, Q
147Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR6 (UCR6)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00127
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 7
G, R
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR7 (CRO1, UCR7)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00128
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 8
H, S
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR8
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P08525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08525
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 9
I, T
66Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR9 (UCR9)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22289
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 10
U, V
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR10
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P37299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P37299
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
a
534Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX1 (OXI3)
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00401 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00401
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
b
251Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX2 (OXI1)
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00410 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00410
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 3
c
269Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX3 (OXI2)
EC: 1.9.3.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00420 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00420
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 4, mitochondrial
d
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX4
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P04037 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04037
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide 5A, mitochondrial
e
153Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX5A
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00424 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: COX5A
Go to UniProtKB:  P00424
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6, mitochondrial
f
148Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX6
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00427 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00427
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 7
g
60Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX7
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P10174 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P10174
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide VIII, mitochondrial
h
78Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX8
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P04039 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04039
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 7A
i
59Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX9
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P07255 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07255
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6B
j
83Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX12
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for Q01519 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q01519
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6A, mitochondrial
k
129Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COX13
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P32799 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32799
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Unknown Cox subunit
m
31N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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Download CCD File 
a
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
7PH
Query on 7PH

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Download CCD File 
D, P
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
PHOSPHATIDIC ACID
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
 Ligand Interaction
CUA
Query on CUA

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Download CCD File 
b
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
6PH
Query on 6PH

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Download CCD File 
C, N
(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
PHOSPHATIDIC ACID
C31 H61 O8 P
UOOPRMYYAWVCCZ-GDLZYMKVSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
E, P
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
C, D, N, O
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CU
Query on CU

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Download CCD File 
a
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CN5
Query on CN5

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Download CCD File 
C
(5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
CARDIOLIPIN
C26 H52 O13 P2
UKWPDXFRXMWSMQ-VWLOTQADSA-N
 Ligand Interaction
PCF
Query on PCF

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Download CCD File 
I, T
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
 Ligand Interaction
8PE
Query on 8PE

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Download CCD File 
C, N
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
RFJQNULIDFTTLL-PGUFJCEWSA-N
 Ligand Interaction
CN3
Query on CN3

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N
(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate
CARDIOLIPIN
C36 H68 O17 P2
FMNZIMGRZPIVKW-XWHIBYANSA-N
 Ligand Interaction
UQ6
Query on UQ6

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Download CCD File 
C, N
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
9PE
Query on 9PE

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Download CCD File 
N
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
3-SN-PHOSPHATIDYLETHANOLAMINE
C30 H60 N O8 P
RWBMCOYSJCETON-MUUNZHRXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
m
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--

Revision History 

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-01-09
    Type: Data collection, Database references
  • Version 1.2: 2019-01-16
    Type: Data collection, Database references
  • Version 1.3: 2019-12-18
    Type: Other