6YMX

CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

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


Literature

Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance.

Berndtsson, J.Aufschnaiter, A.Rathore, S.Marin-Buera, L.Dawitz, H.Diessl, J.Kohler, V.Barrientos, A.Buttner, S.Fontanesi, F.Ott, M.

(2020) EMBO Rep 21: e51015-e51015

  • DOI: 10.15252/embr.202051015
  • Primary Citation of Related Structures:  
    6YMY, 6YMX

  • PubMed Abstract: 
  • Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in various organisms, but their physiological roles remain unclear ...

    Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in various organisms, but their physiological roles remain unclear. Here, we elucidate their function by leveraging a high-resolution structural model of yeast respiratory supercomplexes that allowed us to inhibit supercomplex formation by mutation of key residues in the interaction interface. Analyses of a mutant defective in supercomplex formation, which still contains fully functional individual complexes, show that the lack of supercomplex assembly delays the diffusion of cytochrome c between the separated complexes, thus reducing electron transfer efficiency. Consequently, competitive cellular fitness is severely reduced in the absence of supercomplex formation and can be restored by overexpression of cytochrome c. In sum, our results establish how respiratory supercomplexes increase the efficiency of cellular energy conversion, thereby providing an evolutionary advantage for aerobic organisms.


    Organizational Affiliation

    Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1A [auth a]530Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX1OXI3Q0045
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2B [auth b]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX2OXI1Q0250
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3C [auth c]268Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX3OXI2Q0275
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4, mitochondrialD [auth d]117Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX4YGL187CG1362
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialE [auth e]128Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX5AYNL052WN2474YNL2474W
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6, mitochondrialF [auth f]99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX6YHR051W
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7, mitochondrialG [auth g]55Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX7YMR256CYM9920.10C
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8, mitochondrialH [auth h]51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX8YLR395CL8084.14
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 9, mitochondrialI [auth i]53Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX9YDL067CD2520
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 12, mitochondrialJ [auth j]78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX12YLR038C
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 13, mitochondrialK [auth k]114Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX13YGL191WG1341
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 26, mitochondrialL [auth m]38Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COX26YDR119W-A
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialM [auth A], V [auth L]431Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COR1QCR1YBL045CYBL0403
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialN [auth B], W [auth M]352Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR2COR2UCR2YPR191WP9677.6
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bO [auth C], X [auth N]385Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COBCYTBQ0105
EC: 7.1.1.8
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialP [auth D], Y [auth O]248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CYT1CTC1YOR065WYOR29-16
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialQ [auth E], Z [auth P]185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RIP1YEL024W
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialR [auth F]74Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR6UCR6YFR033C
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7, mitochondrialS [auth G], BA [auth R]126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR7CRO1UCR7YDR529CD9719.32
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8, mitochondrialT [auth H], CA [auth S]93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR8YJL166WJ0526
Membrane Entity: Yes 
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9, mitochondrialU [auth I]54Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR9UCR9YGR183C
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialAA [auth Q]75Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR6UCR6YFR033C
Membrane Entity: Yes 
UniProt
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9, mitochondrialDA [auth T]54Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR9UCR9YGR183C
Membrane Entity: Yes 
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10, mitochondrialEA [auth U]44Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR10YHR001W-AYHR001BW
Membrane Entity: Yes 
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10, mitochondrialFA [auth V]51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR10YHR001W-AYHR001BW
Membrane Entity: Yes 
UniProt
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  • Reference Sequence
Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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HA [auth a], IA [auth a]HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
CN3
Query on CN3

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KA [auth a], MB [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
 Ligand Interaction
PCF
Query on PCF

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GB [auth I], OA [auth c], QA [auth e], RB [auth T], UA [auth m]1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
 Ligand Interaction
PTY
Query on PTY

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DB [auth D], JA [auth a], MA [auth b], NA [auth c], RA [auth i], SA [auth m], TA [auth m]PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
8PE
Query on 8PE

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KB [auth N], YA [auth C](2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
C37 H74 N O8 P
RFJQNULIDFTTLL-PGUFJCEWSA-N
 Ligand Interaction
CN5
Query on CN5

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ZA [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
 Ligand Interaction
HEM
Query on HEM

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CB [auth D], HB [auth N], IB [auth N], OB [auth O], WA [auth C], XA [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
9PE
Query on 9PE

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BB [auth C], LB [auth N](1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
C30 H60 N O8 P
RWBMCOYSJCETON-MUUNZHRXSA-N
 Ligand Interaction
UQ6
Query on UQ6

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AB [auth C], JB [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
 Ligand Interaction
6PH
Query on 6PH

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NB [auth O], VA [auth C](1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
C31 H61 O8 P
UOOPRMYYAWVCCZ-GDLZYMKVSA-N
 Ligand Interaction
7PH
Query on 7PH

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EB [auth E], PB [auth O](1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N
 Ligand Interaction
FES
Query on FES

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FB [auth E], QB [auth P]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
CUA
Query on CUA

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LA [auth b]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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PA [auth d]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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GA [auth a]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2014-4116
Swedish Research CouncilSweden2018-03694
Knut and Alice Wallenberg FoundationSweden2017.0091
Knut and Alice Wallenberg FoundationSweden2013.0006

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references