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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22529 | |||||||||
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Title | Osmoporin OmpC from E.coli K12 | |||||||||
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![]() | Osmoporin OmpC / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.56 Å | |||||||||
![]() | Lyu M / Su C | |||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.9 KB 10.9 KB | Display Display | ![]() |
Images | ![]() | 247.6 KB | ||
Filedesc metadata | ![]() | 4.8 KB | ||
Others | ![]() | 154.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 448.9 KB | Display | ![]() |
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Full document | ![]() | 448.5 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jz3MC ![]() 6wtiC ![]() 6wtzC ![]() 6wu0C ![]() 6wu6C ![]() 7jz2C ![]() 7jz6C ![]() 7jzhC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_22529_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Osmoporin OmpC
Entire | Name: Osmoporin OmpC |
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Components |
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-Supramolecule #1: Osmoporin OmpC
Supramolecule | Name: Osmoporin OmpC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Outer membrane protein C
Macromolecule | Name: Outer membrane protein C / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 38.336242 KDa |
Sequence | String: AEVYNKDGNK LDLYGKVDGL HYFSDNKDVD GDQTYMRLGF KGETQVTDQL TGYGQWEYQI QGNSAENENN SWTRVAFAGL KFQDVGSFD YGRNYGVVYD VTSWTDVLPE FGGDTYGSDN FMQQRGNGFA TYRNTDFFGL VDGLNFAVQY QGKNGNPSGE G FTSGVTNN ...String: AEVYNKDGNK LDLYGKVDGL HYFSDNKDVD GDQTYMRLGF KGETQVTDQL TGYGQWEYQI QGNSAENENN SWTRVAFAGL KFQDVGSFD YGRNYGVVYD VTSWTDVLPE FGGDTYGSDN FMQQRGNGFA TYRNTDFFGL VDGLNFAVQY QGKNGNPSGE G FTSGVTNN GRDALRQNGD GVGGSITYDY EGFGIGGAIS SSKRTDAQNT AAYIGNGDRA ETYTGGLKYD ANNIYLAAQY TQ TYNATRV GSLGWANKAQ NFEAVAQYQF DFGLRPSLAY LQSKGKNLGR GYDDEDILKY VDVGATYYFN KNMSTYVDYK INL LDDNQF TRDAGINTDN IVALGLVYQF UniProtKB: Outer membrane protein C |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68628 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |