6XKZ

R. capsulatus CIII2CIV tripartite super-complex, conformation B (SC-1B)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 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 structures of engineered active bc 1 -cbb 3 type CIII 2 CIV super-complexes and electronic communication between the complexes.

Steimle, S.van Eeuwen, T.Ozturk, Y.Kim, H.J.Braitbard, M.Selamoglu, N.Garcia, B.A.Schneidman-Duhovny, D.Murakami, K.Daldal, F.

(2021) Nat Commun 12: 929-929

  • DOI: https://doi.org/10.1038/s41467-021-21051-4
  • Primary Citation of Related Structures:  
    6XI0, 6XKT, 6XKU, 6XKV, 6XKW, 6XKX, 6XKZ

  • PubMed Abstract: 

    Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc 1 (Complex III, CIII 2 ), and may have specific cbb 3 -type cyt c oxidases (Complex IV, CIV) instead of the canonical aa 3 -type CIV. Electron transfer between these complexes is mediated by soluble (c 2 ) and membrane-anchored (c y ) cyts. Here, we report the structure of an engineered bc 1 -cbb 3 type SC (CIII 2 CIV, 5.2 Å resolution) and three conformers of native CIII 2 (3.3 Å resolution). The SC is active in vivo and in vitro, contains all catalytic subunits and cofactors, and two extra transmembrane helices attributed to cyt c y and the assembly factor CcoH. The cyt c y is integral to SC, its cyt domain is mobile and it conveys electrons to CIV differently than cyt c 2 . The successful production of a native-like functional SC and determination of its structure illustrate the characteristics of membrane-confined and membrane-external respiratory electron transport pathways in Gram-negative bacteria.


  • Organizational Affiliation

    Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunitA [auth E],
F [auth R]
191Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: petAfbcFRCAP_rcc02768
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for D5ANZ2 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5ANZ2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bB [auth C],
D [auth P]
437Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: petBcytBRCAP_rcc02769
Membrane Entity: Yes 
UniProt
Find proteins for D5ANZ3 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5ANZ3
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1C [auth D],
E [auth Q]
279Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: petCRCAP_rcc02770
Membrane Entity: Yes 
UniProt
Find proteins for D5ANZ4 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5ANZ4
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase, Cbb3-type, subunit IG [auth n]532Rhodobacter capsulatus SB 1003Mutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for D5ARP4 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ARP4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase, Cbb3-type, subunit IIH [auth o]242Rhodobacter capsulatus SB 1003Mutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for D5ARP5 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ARP5
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cbb3-type cytochrome c oxidase subunit CcoP,Cytochrome c-type cyt cyI [auth p]474Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: ccoPRCAP_rcc01160cycYRCAP_rcc02501
Membrane Entity: Yes 
UniProt
Find proteins for D5ARP7 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Find proteins for Q05389 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore Q05389 
Go to UniProtKB:  Q05389
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UniProt GroupsD5ARP7Q05389
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
K [auth C]
L [auth C]
M [auth D]
N [auth P]
O [auth P]
K [auth C],
L [auth C],
M [auth D],
N [auth P],
O [auth P],
P [auth Q],
R [auth n],
S [auth n],
U [auth o],
V [auth p],
W [auth p]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
FES
Query on FES

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J [auth E],
Q [auth R]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
T [auth n]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.16

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM38237
Department of Energy (DOE, United States)United StatesDE-FG02-91ER20052
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM123233
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008275
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD023592
Israel Science FoundationIsrael1466/18
United States - Israel Binational Science Foundation (BSF)Israel2016070
Israel Ministry of Science and TechnologyIsrael80802

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references