7JZ6

The Cryo-EM structure of the Catalase-peroxidase from Escherichia coli

  • Classification: OXIDOREDUCTASE
  • Organism(s): Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-09-01 Released: 2021-01-20 
  • Deposition Author(s): Su, C.-C.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: 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 ...

    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. edward.w.yu@case.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Catalase-peroxidaseA, B, C, D726Escherichia coliMutation(s): 0 
Gene Names: 
EC: 1.11.1.21
UniProt
Find proteins for A0A037YMJ1 (Escherichia coli)
Explore A0A037YMJ1 
Go to UniProtKB:  A0A037YMJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A037YMJ1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 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