6WTI

The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.38 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

A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.

Su, C.C.Lyu, M.Morgan, C.E.Bolla, J.R.Robinson, C.V.Yu, E.W.

(2021) Nat Methods 18: 69-75

  • DOI: https://doi.org/10.1038/s41592-020-01021-2
  • Primary Citation of Related Structures:  
    6WTI, 6WTZ, 6WU0, 6WU6, 7JZ2, 7JZ3, 7JZ6, 7JZH

  • PubMed Abstract: 

    Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics.


  • Organizational Affiliation

    Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome o ubiquinol oxidase, subunit I663Escherichia coliMutation(s): 0 
Gene Names: cyoBECDEC2C_0430
EC: 1.10.3 (PDB Primary Data), 7.1.1.3 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P0ABI8 (Escherichia coli (strain K12))
Explore P0ABI8 
Go to UniProtKB:  P0ABI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABI8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol oxidase subunit 2315Escherichia coliMutation(s): 0 
Gene Names: cyoA
Membrane Entity: Yes 
UniProt
Find proteins for P0ABJ1 (Escherichia coli (strain K12))
Explore P0ABJ1 
Go to UniProtKB:  P0ABJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABJ1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome o ubiquinol oxidase204Escherichia coliMutation(s): 0 
Gene Names: ECDG_00226
Membrane Entity: Yes 
UniProt
Find proteins for P0ABJ3 (Escherichia coli (strain K12))
Explore P0ABJ3 
Go to UniProtKB:  P0ABJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABJ3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome o ubiquinol oxidase, subunit IV109Escherichia coliMutation(s): 0 
Gene Names: cyoDEC12741_3890
EC: 1.10.3
Membrane Entity: Yes 
UniProt
Find proteins for P0ABJ6 (Escherichia coli (strain K12))
Explore P0ABJ6 
Go to UniProtKB:  P0ABJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABJ6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEO
Query on HEO

Download Ideal Coordinates CCD File 
F [auth A]HEME O
C49 H58 Fe N4 O5
FRKORVCRVCLRBA-BZKSIRDQSA-L
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
M [auth A]
N [auth B]
I [auth A],
J [auth A],
K [auth A],
M [auth A],
N [auth B],
O [auth C],
P [auth C],
Q [auth D],
R [auth D]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
UQ8
Query on UQ8

Download Ideal Coordinates CCD File 
H [auth A]Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
U9V
Query on U9V

Download Ideal Coordinates CCD File 
L [auth A]pentadecyl(tetradecyl)peroxyanhydride
C33 H64 O4
VKLOIKIKCDJYHU-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2021-01-20 
  • Deposition Author(s): Su, C.-C.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Structure summary