|Entry||Database: PDB / ID: 6wtz|
|Title||Cryo-EM structure of E. Coli OmpF|
|Components||Outer membrane porin F|
|Keywords||MEMBRANE PROTEIN / outer membrane porin / omp / ompf|
|Function / homology|
Function and homology information
colicin transmembrane transporter activity / ion transmembrane transporter activity / ion channel complex / porin activity / pore complex / protein homotrimerization / ion transmembrane transport / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding ...colicin transmembrane transporter activity / ion transmembrane transporter activity / ion channel complex / porin activity / pore complex / protein homotrimerization / ion transmembrane transport / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / ion channel activity / protein N-terminus binding / lipid binding / integral component of membrane / identical protein binding
Porin domain superfamily / Porin domain, Gram-negative type / Porin, Gram-negative type, conserved site / Porin, gammaproteobacterial / Porin, Gram-negative type
Outer membrane porin F
|Biological species||Escherichia coli (E. coli)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å|
|Authors||Morgan, C.E. / Su, C.-C. / Lyu, M. / Yu, E.W.|
|Funding support||1items |
|Citation||Journal: Nat Methods / Year: 2021|
Title: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.
Authors: Chih-Chia Su / Meinan Lyu / Christopher E Morgan / Jani Reddy Bolla / Carol V Robinson / Edward W Yu /
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 ...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.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
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A: Outer membrane porin F
B: Outer membrane porin F
C: Outer membrane porin F
Mass: 39365.043 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02931
|#2: Water|| ChemComp-HOH / |
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: OmpF / Type: COMPLEX / Entity ID: #1 / Source: NATURAL|
|Source (natural)||Organism: Escherichia coli K-12 (bacteria)|
|Buffer solution||pH: 7.5|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: TFS KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)|
|Software||Name: PHENIX / Version: 1.14_3260: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C3 (3 fold cyclic)|
|3D reconstruction||Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43793 / Symmetry type: POINT|
|Refine LS restraints|
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