5LUF

Cryo-EM of bovine respirasome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 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

Functional asymmetry and electron flow in the bovine respirasome.

Sousa, J.S., Mills, D.J., Vonck, J., Kuhlbrandt, W.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.21290
  • Primary Citation of Related Structures:  
    5LUF

  • PubMed Abstract: 

    Respirasomes are macromolecular assemblies of the respiratory chain complexes I, III and IV in the inner mitochondrial membrane. We determined the structure of supercomplex I 1 III 2 IV 1 from bovine heart mitochondria by cryo-EM at 9 Å resolution. Most protein-protein contacts between complex I, III and IV in the membrane are mediated by supernumerary subunits. Of the two Rieske iron-sulfur cluster domains in the complex III dimer, one is resolved, indicating that this domain is immobile and unable to transfer electrons. The central position of the active complex III monomer between complex I and IV in the respirasome is optimal for accepting reduced quinone from complex I over a short diffusion distance of 11 nm, and delivering reduced cytochrome c to complex IV. The functional asymmetry of complex III provides strong evidence for directed electron flow from complex I to complex IV through the active complex III monomer in the mammalian supercomplex.

    • Organizational Affiliation: 

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA [auth c],
L [auth l]		446Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB [auth m],
M [auth n]		439Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23004 (Bos taurus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC [auth b],
N [auth o]		379Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD [auth d],
O [auth p]		241Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE [auth e],
P [auth q]		196Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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UniProt GroupP13272
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F [auth f],
Q [auth r]		110Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G [auth g],
R [auth s]		81Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH [auth h],
S [auth t]		78Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialI [auth i],
T [auth u]		78Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9J [auth j],
U [auth v]		62Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10K [auth k],
V [auth w]		56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1W [auth x]514Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2X [auth y]227Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3Y [auth z]261Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrialZ [auth 1]147Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialAA [auth 2]109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialBA [auth 3]98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialCA [auth 4]84Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1DA [auth 5]85Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CEA [auth 6]73Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialFA [auth 7]59Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrialGA [auth 8]56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialHA [auth 9]47Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrialIA [auth 0]46Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
complex IJA [auth A]111Bos taurusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
complex IKA [auth B]143Bos taurusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
complex ILA [auth C]154Bos taurusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
complex IMA [auth D]384Bos taurusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
complex INA [auth E]159Bos taurusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
complex IOA [auth F]411Bos taurusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
complex IPA [auth G]538Bos taurusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
complex IQA [auth H]313Bos taurusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
complex IRA [auth I]162Bos taurusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
complex ISA [auth J]171Bos taurusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
complex ITA [auth K]84Bos taurusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
complex IUA [auth L]601Bos taurusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
complex IVA [auth M]453Bos taurusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
complex IWA [auth N]345Bos taurusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
complex IXA [auth O]220Bos taurusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
complex IYA [auth P]303Bos taurusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
complex IZA [auth Q]85Bos taurusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
complex IAB [auth R]47Bos taurusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
complex IBB [auth S]80Bos taurusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
complex ICB [auth T]75Bos taurusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
complex IDB [auth V]71Bos taurusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
complex IEB [auth W]72Bos taurusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
complex IFB [auth X]330Bos taurusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
complex IGB [auth Y]106Bos taurusMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
complex IHB [auth a]142Bos taurusMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
complex IIB [auth U]828Bos taurusMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
complex IJB [auth Z]625Bos taurusMutation(s): 0 
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA
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TB [auth x],
UB [auth x]		HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
HEC
Query on HEC
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MB [auth d],
PB [auth p]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM
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KB [auth b],
LB [auth b],
NB [auth o],
OB [auth o]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4
Query on SF4
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AC [auth F]
BC [auth G]
CC [auth G]
EC [auth I]
FC [auth I]
AC [auth F],
BC [auth G],
CC [auth G],
EC [auth I],
FC [auth I],
YB [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
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DC [auth G],
QB [auth q],
ZB [auth E]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
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XB [auth 3]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
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RB [auth x],
VB [auth y],
WB [auth y]		COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG
Query on MG
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SB [auth x]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Other