+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42462 | |||||||||
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Title | Human Plasminogen bound to streptococcal surface enolase | |||||||||
Map data | Main map of human plasminogen bound to SEN on the surface of a lipid | |||||||||
Sample |
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Keywords | Glycolysis / plasminogen binder / membrane protein / LYASE | |||||||||
Function / homology | Function and homology information plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / myoblast differentiation / negative regulation of cell-substrate adhesion / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / Schaffer collateral - CA1 synapse / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / endopeptidase activity / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Tjia-Fleck S / Readnour BM / Castellino FJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Streptococcus surface alpha enolase exposed dimers were found to be the active form on lipid surface that binds to human plasminogen Authors: Tjia-Fleck S / Readnour BM / Castellino FJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42462.map.gz | 135.6 MB | EMDB map data format | |
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Header (meta data) | emd-42462-v30.xml emd-42462.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42462_fsc.xml | 11.2 KB | Display | FSC data file |
Images | emd_42462.png | 44.3 KB | ||
Filedesc metadata | emd-42462.cif.gz | 5.9 KB | ||
Others | emd_42462_half_map_1.map.gz emd_42462_half_map_2.map.gz | 134.2 MB 134.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42462 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42462 | HTTPS FTP |
-Validation report
Summary document | emd_42462_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_42462_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_42462_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_42462_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42462 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42462 | HTTPS FTP |
-Related structure data
Related structure data | 8uq6MC 8uopC 8uoyC 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_42462.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main map of human plasminogen bound to SEN on the surface of a lipid | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.539 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map A of human plasminogen bound to...
File | emd_42462_half_map_1.map | ||||||||||||
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Annotation | half map A of human plasminogen bound to SEN on the surface of a lipid | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B of human plasminogen bound to...
File | emd_42462_half_map_2.map | ||||||||||||
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Annotation | half map B of human plasminogen bound to SEN on the surface of a lipid | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human plasminogen bound to streptococcal enolase on the surface o...
Entire | Name: Human plasminogen bound to streptococcal enolase on the surface of a lipid vesicle |
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Components |
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-Supramolecule #1: Human plasminogen bound to streptococcal enolase on the surface o...
Supramolecule | Name: Human plasminogen bound to streptococcal enolase on the surface of a lipid vesicle type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 91 KDa |
-Macromolecule #1: Plasminogen
Macromolecule | Name: Plasminogen / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 88.544461 KDa |
Recombinant expression | Organism: Drosophila (fruit flies) |
Sequence | String: EPLDDYVNTQ GASLFSVTKK QLGAGSIEEC AAKCEEDEEF TCRAFQYHSK EQQCVIMAEN RKSSIIIRMR DVVLFEKKVY LSECKTGNG KNYRGTMSKT KNGITCQKWS STSPHRPRFS PATHPSEGLE ENYCRNPDND PQGPWCYTTD PEKRYDYCDI L ECEEECMH ...String: EPLDDYVNTQ GASLFSVTKK QLGAGSIEEC AAKCEEDEEF TCRAFQYHSK EQQCVIMAEN RKSSIIIRMR DVVLFEKKVY LSECKTGNG KNYRGTMSKT KNGITCQKWS STSPHRPRFS PATHPSEGLE ENYCRNPDND PQGPWCYTTD PEKRYDYCDI L ECEEECMH CSGENYDGKI SKTMSGLECQ AWDSQSPHAH GYIPSKFPNK NLKKNYCRNP DRELRPWCFT TDPNKRWELC DI PRCTTPP PSSGPTYQCL KGTGENYRGN VAVTVSGHTC QHWSAQTPHT HNRTPENFPC KNLDENYCRN PDGKRAPWCH TTN SQVRWE YCKIPSCDSS PVSTEQLAPT APPELTPVVQ DCYHGDGQSY RGTSSTTTTG KKCQSWSSMT PHRHQKTPEN YPNA GLTMN YCRNPDADKG PWCFTTDPSV RWEYCNLKKC SGTEASVVAP PPVVLLPDVE TPSEEDCMFG NGKGYRGKRA TTVTG TPCQ DWAAQEPHRH SIFTPETNPR AGLEKNYCRN PDGDVGGPWC YTTNPRKLYD YCDVPQCAAP SFDCGKPQVE PKKCPG RVV GGCVAHPHSW PWQVSLRTRF GMHFCGGTLI SPEWVLTAAH CLEKSPRPSS YKVILGAHQE VNLEPHVQEI EVSRLFL EP TRKDIALLKL SSPAVITDKV IPACLPSPNY VVADRTECFI TGWGETQGTF GAGLLKEAQL PVIENKVCNR YEFLNGRV Q STELCAGHLA GGTDSCQGDS GGPLVCFEKD KYILQGVTSW GLGCARPNKP GVYVRVSRFV TWIEGVMRNN UniProtKB: Plasminogen |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: C-flat-1.2/1.3 / Material: GOLD |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4776 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |