6BTM

Structure of Alternative Complex III from Flavobacterium johnsoniae (Wild Type)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structure of the alternative complex III in a supercomplex with cytochrome oxidase.

Sun, C.Benlekbir, S.Venkatakrishnan, P.Wang, Y.Hong, S.Hosler, J.Tajkhorshid, E.Rubinstein, J.L.Gennis, R.B.

(2018) Nature 557: 123-126

  • DOI: 10.1038/s41586-018-0061-y
  • Primary Citation of Related Structures:  
    6BTM

  • PubMed Abstract: 
  • Alternative complex III (ACIII) is a key component of the respiratory and/or photosynthetic electron transport chains of many bacteria 1-3 . Like complex III (also known as the bc 1 complex), ACIII catalyses the oxidation of membrane-bound quinol and the reduction of cytochrome c or an equivalent electron carrier ...

    Alternative complex III (ACIII) is a key component of the respiratory and/or photosynthetic electron transport chains of many bacteria 1-3 . Like complex III (also known as the bc 1 complex), ACIII catalyses the oxidation of membrane-bound quinol and the reduction of cytochrome c or an equivalent electron carrier. However, the two complexes have no structural similarity 4-7 . Although ACIII has eluded structural characterization, several of its subunits are known to be homologous to members of the complex iron-sulfur molybdoenzyme (CISM) superfamily 8 , including the proton pump polysulfide reductase 9,10 . We isolated the ACIII from Flavobacterium johnsoniae with native lipids using styrene maleic acid copolymer 11-14 , both as an independent enzyme and as a functional 1:1 supercomplex with an aa 3 -type cytochrome c oxidase (cyt aa 3 ). We determined the structure of ACIII to 3.4 Å resolution by cryo-electron microscopy and constructed an atomic model for its six subunits. The structure, which contains a [3Fe-4S] cluster, a [4Fe-4S] cluster and six haem c units, shows that ACIII uses known elements from other electron transport complexes arranged in a previously unknown manner. Modelling of the cyt aa 3 component of the supercomplex revealed that it is structurally modified to facilitate association with ACIII, illustrating the importance of the supercomplex in this electron transport chain. The structure also resolves two of the subunits of ACIII that are anchored to the lipid bilayer with N-terminal triacylated cysteine residues, an important post-translational modification found in numerous prokaryotic membrane proteins that has not previously been observed structurally in a lipid bilayer.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois, Urbana, IL, USA. r-gennis@illinois.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alternative Complex III subunit AA444Flavobacterium johnsoniae UW101Mutation(s): 0 
Gene Names: Fjoh_1634
UniProt
Find proteins for A5FJF1 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101))
Explore A5FJF1 
Go to UniProtKB:  A5FJF1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Alternative Complex III subunit BB948Flavobacterium johnsoniae UW101Mutation(s): 0 
Gene Names: Fjoh_1635
UniProt
Find proteins for A5FJF2 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101))
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Go to UniProtKB:  A5FJF2
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Alternative Complex III subunit CC466Flavobacterium johnsoniae UW101Mutation(s): 0 
Gene Names: Fjoh_1636
Membrane Entity: Yes 
UniProt
Find proteins for A5FJF3 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101))
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Go to UniProtKB:  A5FJF3
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Alternative Complex III subunit DD174Flavobacterium johnsoniae UW101Mutation(s): 0 
Gene Names: Fjoh_1637
UniProt
Find proteins for A5FJF4 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101))
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Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Alternative Complex III subunit EE161Flavobacterium johnsoniae UW101Mutation(s): 0 
Gene Names: Fjoh_1638
UniProt
Find proteins for A5FJF5 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101))
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Protein Feature View
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Alternative Complex III subunit FF464Flavobacterium johnsoniae UW101Mutation(s): 0 
Gene Names: Fjoh_1639
UniProt
Find proteins for A5FJE2 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101))
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Go to UniProtKB:  A5FJE2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E87
Query on E87

Download Ideal Coordinates CCD File 
N [auth B], P [auth E](2R)-3-{[(2R)-2-(decanoylamino)-3-hydroxypropyl]sulfanyl}propane-1,2-diyl ditetradecanoate
C44 H85 N O6 S
XFKPIMKYVGTUPF-GYOJGHLZSA-N
 Ligand Interaction
HEC
Query on HEC

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth E]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
M [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
L [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01-HL16101
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41-GM104601
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54-GM087519
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM123455
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
National Institutes of Health/Office of the DirectorUnited StatesOD019994
Simons FoundationUnited States349247
Canadian Institutes of Health Research (CIHR)CanadaMOP-81294

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 2.0: 2019-02-20
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.2: 2019-12-18
    Changes: Author supporting evidence, Other