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Yorodumi- EMDB-42429: Plasminogen binding group A streptococcus M-like protein from AP5... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42429 | ||||||||||||
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Title | Plasminogen binding group A streptococcus M-like protein from AP53 bound to human plasminogen | ||||||||||||
Map data | Full Map of hPg bound to PAM on a lentivirus | ||||||||||||
Sample |
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Keywords | PAM / human plasminogen / M-protein / Group A streptococcus / BLOOD CLOTTING | ||||||||||||
Function / homology | : / Streptococcal M proteins D repeats region profile. / : / Streptococcal M proteins C repeat profile. / Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / YSIRK Gram-positive signal peptide / extracellular region / M protein Function and homology information | ||||||||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||
Authors | Readnour BM / Tjia-Fleck SK / Castellino FJ / McCann NR | ||||||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Plasminogen binding group A streptococcus M-like protein from AP53 bound to human plasminogen Authors: Readnour BM / Tjia-Fleck SK / McCann NR / Ayinuola YA / Ploplis VA / Castellino FJ | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42429.map.gz | 166.9 MB | EMDB map data format | |
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Header (meta data) | emd-42429-v30.xml emd-42429.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42429_fsc.xml | 12 KB | Display | FSC data file |
Images | emd_42429.png | 80.7 KB | ||
Filedesc metadata | emd-42429.cif.gz | 5 KB | ||
Others | emd_42429_half_map_1.map.gz emd_42429_half_map_2.map.gz | 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42429 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42429 | HTTPS FTP |
-Validation report
Summary document | emd_42429_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_42429_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_42429_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | emd_42429_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42429 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42429 | HTTPS FTP |
-Related structure data
Related structure data | 8tvlMC 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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-Map
File | Download / File: emd_42429.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Full Map of hPg bound to PAM on a lentivirus | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.437 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map of hPg bound to PAM on a lentivirus
File | emd_42429_half_map_1.map | ||||||||||||
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Annotation | Half Map of hPg bound to PAM on a lentivirus | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map of hPg bound to PAM on a lentivirus
File | emd_42429_half_map_2.map | ||||||||||||
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Annotation | Half Map of hPg bound to PAM on a lentivirus | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Plasminogen Binding Group A Streptococcus M-Like Protein from AP5...
Entire | Name: Plasminogen Binding Group A Streptococcus M-Like Protein from AP53 bound to human plasminogen |
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Components |
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-Supramolecule #1: Plasminogen Binding Group A Streptococcus M-Like Protein from AP5...
Supramolecule | Name: Plasminogen Binding Group A Streptococcus M-Like Protein from AP53 bound to human plasminogen type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: PAM was bound to the surface of a lentivirus |
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Source (natural) | Organism: Streptococcus pyogenes (bacteria) / Strain: AP53 / Location in cell: Cell surface |
Molecular weight | Theoretical: 41 KDa |
-Macromolecule #1: Plasminogen binding group A streptococcus M-like protein
Macromolecule | Name: Plasminogen binding group A streptococcus M-like protein type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Streptococcus pyogenes (bacteria) / Strain: AP53 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MNRADDARNE VLRGNLVRAE LWYRQIQEND QL KLENKGL KTDLREKEEE LQGLKDDVEK LTADAELQRL KNERHEEAEL ERLKSERHDH DKK EAERKA LEDKLADKQE HLNGALRYIN EKEAEAKEKE AEQKKLKEEK QISDASRQGL RRDL DASRE AKKQVEKDLA ...String: MNRADDARNE VLRGNLVRAE LWYRQIQEND QL KLENKGL KTDLREKEEE LQGLKDDVEK LTADAELQRL KNERHEEAEL ERLKSERHDH DKK EAERKA LEDKLADKQE HLNGALRYIN EKEAEAKEKE AEQKKLKEEK QISDASRQGL RRDL DASRE AKKQVEKDLA NLTAELDKVK EEKQISDASR QGLRRDLDAS REAKKQVEKG LANLT AELD KVKEEKQISD ASRQGLRRDL DASREAKKQV EKALEEANSK LAALEKLNKE LEESKK LTE KEKAELQAKL EAEAKALKEQ LAKQAEELAK LRAEKASDSQ TPDAKPGNKA VPGKGQA PQ AGTKPNQNKA PMKETKRQLP STG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Formula: PBS |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
Details | Plasminogen binding Group A streptococcus M like protein of AP53 bound to human plasminogen on the surface of a lentivirus |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 4054 / Average electron dose: 55.0 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: 34.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 109000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8tvl: |