6RKO

Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Active site rearrangement and structural divergence in prokaryotic respiratory oxidases.

Safarian, S.Hahn, A.Mills, D.J.Radloff, M.Eisinger, M.L.Nikolaev, A.Meier-Credo, J.Melin, F.Miyoshi, H.Gennis, R.B.Sakamoto, J.Langer, J.D.Hellwig, P.Kuhlbrandt, W.Michel, H.

(2019) Science 366: 100-104

  • DOI: https://doi.org/10.1126/science.aay0967
  • Primary Citation of Related Structures:  
    6RKO

  • PubMed Abstract: 

    Cytochrome bd-type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial cytochrome c oxidases and are therefore a prime target for the development of antimicrobial drugs. We determined the structure of the Escherichia coli cytochrome bd-I oxidase by single-particle cryo-electron microscopy to a resolution of 2.7 angstroms. Our structure contains a previously unknown accessory subunit CydH, the L-subfamily-specific Q-loop domain, a structural ubiquinone-8 cofactor, an active-site density interpreted as dioxygen, distinct water-filled proton channels, and an oxygen-conducting pathway. Comparison with another cytochrome bd oxidase reveals structural divergence in the family, including rearrangement of high-spin hemes and conformational adaption of a transmembrane helix to generate a distinct oxygen-binding site.


  • Organizational Affiliation

    Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, D-60438 Frankfurt/Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bd-I ubiquinol oxidase subunit 2A [auth B]379Escherichia coli K-12Mutation(s): 0 
Gene Names: cydBcyd-2b0734JW0723
EC: 7.1.1.7
Membrane Entity: Yes 
UniProt
Find proteins for P0ABK2 (Escherichia coli (strain K12))
Explore P0ABK2 
Go to UniProtKB:  P0ABK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABK2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bd-I ubiquinol oxidase subunit 1B [auth A]522Escherichia coli K-12Mutation(s): 0 
Gene Names: cydAcyd-1b0733JW0722
EC: 7.1.1.7
Membrane Entity: Yes 
UniProt
Find proteins for P0ABJ9 (Escherichia coli (strain K12))
Explore P0ABJ9 
Go to UniProtKB:  P0ABJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABJ9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein YnhFC [auth H]29Escherichia coli K-12Mutation(s): 0 
Gene Names: ynhFb4602JW1649.1
Membrane Entity: Yes 
UniProt
Find proteins for A5A618 (Escherichia coli (strain K12))
Explore A5A618 
Go to UniProtKB:  A5A618
Entity Groups  
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UniProt GroupA5A618
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bd-I ubiquinol oxidase subunit XD [auth X]37Escherichia coli K-12Mutation(s): 0 
Gene Names: cydXybgTb4515JW0724
EC: 7.1.1.7
Membrane Entity: Yes 
UniProt
Find proteins for P56100 (Escherichia coli (strain K12))
Explore P56100 
Go to UniProtKB:  P56100
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UniProt GroupP56100
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
F [auth B],
G [auth B],
H [auth A],
I [auth A]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
UQ8
Query on UQ8

Download Ideal Coordinates CCD File 
E [auth B]Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
HDD
Query on HDD

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J [auth A]CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
C34 H32 Fe N4 O5
UMGOPAWIGKFTRK-QQDQPIDJSA-N
HEB
Query on HEB

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A]
HEME B/C
C34 H34 Fe N4 O4
NEGHHAJBRZGUAY-RGGAHWMASA-L
OXY
Query on OXY

Download Ideal Coordinates CCD File 
M [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-18
    Changes: Other
  • Version 1.4: 2024-05-22
    Changes: Data collection, Database references, Structure summary