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 6GIQ | pdb_00006giq

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

Validation slider image for 6GIQ

This is version 3.1 of the entry. See complete history. 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6YMX 6YMY

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: https://doi.org/10.1038/s41594-018-0169-7
  • Primary Citation Related Structures: 
    6GIQ

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 736.66 kDa 
  • Atom Count: 44,120 
  • Modeled Residue Count: 5,470 
  • Deposited Residue Count: 6,440 
  • Unique protein chains: 22

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0001550.mRNA.1.CDS.1A,
J [auth L]
457Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB,
K [auth M]
368Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bC,
L [auth N]
385Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0049990.mRNA.1.CDS.1D,
M [auth O]
309Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for A0A5B9RH60 (Saccharomyces cerevisiae)
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Go to UniProtKB:  A0A5B9RH60
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UniProt GroupA0A5B9RH60
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE,
N [auth P]
215Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
QCR6 isoform 1F,
O [auth Q]
147Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Complex III subunit 7G,
P [auth R]
127Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0028260.mRNA.1.CDS.1H,
Q [auth S]
94Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
HLJ1_G0021680.mRNA.1.CDS.1I,
R [auth T]
66Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0023510.mRNA.1.CDS.1S [auth U],
T [auth V]
77Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1U [auth a]534Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P00401 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00401 
Go to UniProtKB:  P00401
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UniProt GroupP00401
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2V [auth b]251Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3W [auth c]269Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0018620.mRNA.1.CDS.1X [auth d]155Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0046460.mRNA.1.CDS.1Y [auth e]153Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0024040.mRNA.1.CDS.1Z [auth f]148Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0043230.mRNA.1.CDS.1AA [auth g]60Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0038800.mRNA.1.CDS.1BA [auth h]78Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIIACA [auth i]59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
BJ4_G0035470.mRNA.1.CDS.1DA [auth j]83Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunitEA [auth k]129Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown Cox subunitFA [auth m]31Saccharomyces cerevisiaeMutation(s): 0 
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Reference Sequence

Small Molecules

Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA

Query on HEA



Download:Ideal Coordinates CCD File
DB [auth a],
EB [auth a]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
CN3

Query on CN3



Download:Ideal Coordinates CCD File
XA [auth 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
C36 H68 O17 P2
FMNZIMGRZPIVKW-XWHIBYANSA-N
PCF

Query on PCF



Download:Ideal Coordinates CCD File
BB [auth T],
PA [auth I]
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
8PE

Query on 8PE



Download:Ideal Coordinates CCD File
JA [auth C],
VA [auth N]
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
C37 H74 N O8 P
RFJQNULIDFTTLL-PGUFJCEWSA-N
CN5

Query on CN5



Download:Ideal Coordinates CCD File
KA [auth C](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
HEC

Query on HEC



Download:Ideal Coordinates CCD File
HA [auth C]
IA [auth C]
MA [auth D]
SA [auth N]
TA [auth N]
HA [auth C],
IA [auth C],
MA [auth D],
SA [auth N],
TA [auth N],
YA [auth O]
HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
9PE

Query on 9PE



Download:Ideal Coordinates CCD File
QA [auth N],
WA [auth N]
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
C30 H60 N O8 P
RWBMCOYSJCETON-MUUNZHRXSA-N
UQ6

Query on UQ6



Download:Ideal Coordinates CCD File
LA [auth C],
UA [auth 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
6PH

Query on 6PH



Download:Ideal Coordinates CCD File
GA [auth C],
RA [auth N]
(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
C31 H61 O8 P
UOOPRMYYAWVCCZ-GDLZYMKVSA-N
7PH

Query on 7PH



Download:Ideal Coordinates CCD File
NA [auth D],
ZA [auth P]
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
AB [auth P],
OA [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CUA

Query on CUA



Download:Ideal Coordinates CCD File
FB [auth b]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
CB [auth a]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Non-standard Monomers  1 Unique
IDChains TypeFormula2D Diagram
UNK
Query on UNK
L-PEPTIDE LINKINGC4 H9 N O2

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-01-09
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Other
  • Version 2.0: 2024-10-09
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
  • Version 3.0: 2026-08-26
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2026-09-16
    Changes: Data collection