6WTZ | pdb_00006wtz

Cryo-EM structure of E. Coli OmpF


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6WTZ

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 118.1 kDa 
  • Atom Count: 7,917 
  • Modeled Residue Count: 1,020 
  • Deposited Residue Count: 1,086 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane porin F
A, B, C
362Escherichia coli K-12Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02931 (Escherichia coli (strain K12))
Explore P02931 
Go to UniProtKB:  P02931
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02931
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


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

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
  • Version 1.2: 2025-05-14
    Changes: Data collection, Structure summary