8ASJ

Four subunit cytochrome b-c1 complex from Rhodobacter sphaeroides in native nanodiscs - focussed refinement in the b-c conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 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


Literature

Cryo-EM structure of the four-subunit Rhodobacter sphaeroides cytochrome bc 1 complex in styrene maleic acid nanodiscs.

Swainsbury, D.J.K.Hawkings, F.R.Martin, E.C.Musial, S.Salisbury, J.H.Jackson, P.J.Farmer, D.A.Johnson, M.P.Siebert, C.A.Hitchcock, A.Hunter, C.N.

(2023) Proc Natl Acad Sci U S A 120: e2217922120-e2217922120

  • DOI: https://doi.org/10.1073/pnas.2217922120
  • Primary Citation of Related Structures:  
    8ASI, 8ASJ

  • PubMed Abstract: 

    Cytochrome bc 1 complexes are ubiquinol:cytochrome c oxidoreductases, and as such, they are centrally important components of respiratory and photosynthetic electron transfer chains in many species of bacteria and in mitochondria. The minimal complex has three catalytic components, which are cytochrome b , cytochrome c 1 , and the Rieske iron-sulfur subunit, but the function of mitochondrial cytochrome bc 1 complexes is modified by up to eight supernumerary subunits. The cytochrome bc 1 complex from the purple phototrophic bacterium Rhodobacter   sphaeroides has a single supernumerary subunit called subunit IV, which is absent from current structures of the complex. In this work we use the styrene-maleic acid copolymer to purify the R. sphaeroides cytochrome bc 1 complex in native lipid nanodiscs, which retains the labile subunit IV, annular lipids, and natively bound quinones. The catalytic activity of the four-subunit cytochrome bc 1 complex is threefold higher than that of the complex lacking subunit IV. To understand the role of subunit IV, we determined the structure of the four-subunit complex at 2.9 Å using single particle cryogenic electron microscopy. The structure shows the position of the transmembrane domain of subunit IV, which lies across the transmembrane helices of the Rieske and cytochrome c 1 subunits. We observe a quinone at the Q o quinone-binding site and show that occupancy of this site is linked to conformational changes in the Rieske head domain during catalysis. Twelve lipids were structurally resolved, making contacts with the Rieske and cytochrome b subunits, with some spanning both of the two monomers that make up the dimeric complex.


  • Organizational Affiliation

    School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunit
A, E
187Cereibacter sphaeroides 2.4.1Mutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for Q3IY09 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3IY09 
Go to UniProtKB:  Q3IY09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3IY09
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b
B, F
445Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3IY10 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3IY10 
Go to UniProtKB:  Q3IY10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3IY10
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1
C, G
285Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3IY11 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3IY11 
Go to UniProtKB:  Q3IY11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3IY11
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 subunit IV
D, H
124Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q3J2Z2 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3J2Z2 
Go to UniProtKB:  Q3J2Z2
Entity Groups  
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UniProt GroupQ3J2Z2
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U10 (Subject of Investigation/LOI)
Query on U10

Download Ideal Coordinates CCD File 
BA [auth F]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PEE (Subject of Investigation/LOI)
Query on PEE

Download Ideal Coordinates CCD File 
AA [auth F]
J [auth A]
M [auth B]
N [auth B]
O [auth B]
AA [auth F],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
U [auth E],
X [auth F],
Y [auth F],
Z [auth F]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

Download Ideal Coordinates CCD File 
CA [auth G],
S [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B],
V [auth F],
W [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
I [auth A],
T [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union854126
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M000265/1
Wellcome TrustUnited Kingdomnr29785
Royal SocietyUnited KingdomURF/R1/19154
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V006630/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references