6KLV

Hyperthermophilic respiratory Complex III


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A 3.3 angstrom -Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability.

Zhu, G.Zeng, H.Zhang, S.Juli, J.Pang, X.Hoffmann, J.Zhang, Y.Morgner, N.Zhu, Y.Peng, G.Michel, H.Sun, F.

(2020) Angew Chem Int Ed Engl 59: 343-351

  • DOI: https://doi.org/10.1002/anie.201911554
  • Primary Citation of Related Structures:  
    6KLS, 6KLV

  • PubMed Abstract: 

    Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc 1 complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc 1 complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Å resolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N-terminus of cyt. c 1 was found to greatly enhance the interaction between cyt. b and cyt. c 1 , and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc 1 complex in an extreme thermal environment.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rieske-I iron sulfur protein
A, D
181Aquifex aeolicus VF5Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O66460 (Aquifex aeolicus (strain VF5))
Explore O66460 
Go to UniProtKB:  O66460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66460
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b
B, E
410Aquifex aeolicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O66459 (Aquifex aeolicus (strain VF5))
Explore O66459 
Go to UniProtKB:  O66459
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66459
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c
C, F
240Aquifex aeolicus VF5Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O66458 (Aquifex aeolicus (strain VF5))
Explore O66458 
Go to UniProtKB:  O66458
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66458
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGV
Query on PGV

Download Ideal Coordinates CCD File 
M [auth B],
N [auth B],
V [auth E]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
DLX
Query on DLX

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
Q [auth D],
U [auth E]
2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione
C45 H66 O2
HQTZEMLTZXAZEE-ZTUUOAHYSA-N
HEC
Query on HEC

Download Ideal Coordinates CCD File 
O [auth C],
W [auth F]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
R [auth E],
S [auth E]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
AMY
Query on AMY

Download Ideal Coordinates CCD File 
K [auth B],
T [auth E]
ANTIMYCIN
C27 H38 N2 O9
ZVYMCLIDNNTNCL-BJDKEMKCSA-N
FES
Query on FES

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 2.0: 2021-04-07
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Data collection, Derived calculations