+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22529 | |||||||||
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Title | Osmoporin OmpC from E.coli K12 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Osmoporin OmpC / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.56 Å | |||||||||
Authors | Lyu M / Su C | |||||||||
Funding support | United States, 1 items
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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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22529.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-22529-v30.xml emd-22529.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_22529.png | 247.6 KB | ||
Filedesc metadata | emd-22529.cif.gz | 4.8 KB | ||
Others | emd_22529_additional_1.map.gz | 154.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22529 | HTTPS FTP |
-Validation report
Summary document | emd_22529_validation.pdf.gz | 448.9 KB | Display | EMDB validaton report |
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Full document | emd_22529_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | emd_22529_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | emd_22529_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22529 | 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 (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22529.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
-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: Escherichia coli (E. coli) / Strain: K-12 |
-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: Escherichia coli (E. coli) / Strain: K-12 |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-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 |