+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26406 | |||||||||
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Title | Structure of enolase from Streptococcus Pyogenes | |||||||||
Map data | Image of Cryo-Em Map of Octameric streptococcal Enolase | |||||||||
Sample |
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Keywords | metalloenzyme / lyase / hPg-Receptor | |||||||||
Function / homology | Function and homology information phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / peptidoglycan-based cell wall / glycolytic process / cell surface / magnesium ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Streptococcus pyogenes (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Tjia-Fleck S / Readnour B / Castellino FJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Biochemistry / Year: 2023 Title: High-Resolution Single-Particle Cryo-EM Hydrated Structure of Enolase Offers Insights into Its Function as a Plasminogen Receptor. Authors: Sheiny Tjia-Fleck / Bradley M Readnour / Yetunde A Ayinuola / Francis J Castellino / Abstract: Cellular plasminogen (Pg) receptors (PgRs) are utilized to recruit Pg; stimulate its activation to the serine protease, plasmin (Pm); and sterically protect the surface Pm from inactivation by host ...Cellular plasminogen (Pg) receptors (PgRs) are utilized to recruit Pg; stimulate its activation to the serine protease, plasmin (Pm); and sterically protect the surface Pm from inactivation by host inhibitors. One such PgR is the moonlighting enzyme, enolase, some of which leaves the cytoplasm and resides at the cell surface to potentially function as a PgR. Since microbes employ conscription of host Pg by PgRs as one virulence mechanism, we explored the structural basis of the ability of enolase (Sen) to function in this manner. Employing single-particle cryo-electron microscopy (cryo-EM), recombinant Sen from was modeled at 2.6 Å as a stable symmetrical doughnut-shaped homooctamer with point group 422 (D4) symmetry, with a monomeric subunit molecular weight of ∼49 kDa. Binding sites for hPg were reported in other studies to include an internal K and the COOH-terminal K residues of Sen. However, in native Sen, the latter are buried within the minor interfaces of the octamer and do not function as a Pg-binding epitope. Whereas Sen and hPg do not interact in solution, when Sen is bound to a surface, hPg interacts with Sen independently of K. PgRs devoid of COOH-terminal lysine utilize lysine isosteres comprising a basic residue, "", and an anionic residue at " + 3" around one turn of an α-helix. We highlight a number of surface-exposed potential hPg-binding lysine isosteres and further conclude that while the octameric structure of Sen is critical for hPg binding, disruption of this octamer without dissociation exposes hPg-binding epitopes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26406.map.gz | 6.3 MB | EMDB map data format | |
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Header (meta data) | emd-26406-v30.xml emd-26406.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26406_fsc.xml | 11.6 KB | Display | FSC data file |
Images | emd_26406.png | 133.5 KB | ||
Masks | emd_26406_msk_1.map | 64 MB | Mask map | |
Others | emd_26406_half_map_1.map.gz emd_26406_half_map_2.map.gz | 6.3 MB 6.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26406 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26406 | HTTPS FTP |
-Validation report
Summary document | emd_26406_validation.pdf.gz | 593.9 KB | Display | EMDB validaton report |
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Full document | emd_26406_full_validation.pdf.gz | 593.5 KB | Display | |
Data in XML | emd_26406_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_26406_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26406 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26406 | HTTPS FTP |
-Related structure data
Related structure data | 7uguMC 8dg4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26406.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Image of Cryo-Em Map of Octameric streptococcal Enolase | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.29052 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26406_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half Cryo-Em Map 1 of Octameric streptococcal Enolase
File | emd_26406_half_map_1.map | ||||||||||||
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Annotation | Half Cryo-Em Map 1 of Octameric streptococcal Enolase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Cryo-Em Map 2 of Octameric streptococcal Enolase
File | emd_26406_half_map_2.map | ||||||||||||
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Annotation | Half Cryo-Em Map 2 of Octameric streptococcal Enolase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Octameric structure of Enolase from Streoptococcus Pyogenes
Entire | Name: Octameric structure of Enolase from Streoptococcus Pyogenes |
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Components |
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-Supramolecule #1: Octameric structure of Enolase from Streoptococcus Pyogenes
Supramolecule | Name: Octameric structure of Enolase from Streoptococcus Pyogenes type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Streptococcus pyogenes (bacteria) / Strain: AP53 |
Molecular weight | Theoretical: 400 KDa |
-Macromolecule #1: Streptococcal Surface Enolase
Macromolecule | Name: Streptococcal Surface Enolase / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Streptococcus pyogenes (bacteria) / Strain: AP53 |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: HMSIITDVYA REVLDSRGNP TLEVEVYTES GAFGRGMVPS GASTGEHEAV ELRDGDKSRY LGLGTQKAVD NVNNIIAEAI IGYDVRDQQA IDRAMIALDG TPNKGKLGAN AILGVSIAVA RAAADYLEVP LYTYLGGFNT KVLPTPMMNI INGGSHSDAP IAFQEFMIMP ...String: HMSIITDVYA REVLDSRGNP TLEVEVYTES GAFGRGMVPS GASTGEHEAV ELRDGDKSRY LGLGTQKAVD NVNNIIAEAI IGYDVRDQQA IDRAMIALDG TPNKGKLGAN AILGVSIAVA RAAADYLEVP LYTYLGGFNT KVLPTPMMNI INGGSHSDAP IAFQEFMIMP VGAPTFKEGL RWGAEVFHAL KKILKERGLV TAVGDEGGFA PKFEGTEDGV ETILKAIEAA GYEAGENGIM IGFDCASSEF YDKERKVYDY TKFEGEGAAV RTSAEQVDYL EELVNKYPII TIEDGMDEND WDGWKVLTER LGKRVQLVGD DFFVTNTEYL ARGIKENAAN SILIKVNQIG TLTETFEAIE MAKEAGYTAV VSHRSGETED STIADIAVAT NAGQIKTGSL SRTDRIAKYN QLLRIEDQLG EVAQYKGIKS FYNLKK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 0.05 mM / Component - Formula: NaH2PO4 / Component - Name: Sodium phospate |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 1 / Number real images: 2756 / Average electron dose: 61.37 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |