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Yorodumi- PDB-8tvl: Plasminogen binding group A streptococcus M-like protein from AP5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tvl | ||||||
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Title | Plasminogen binding group A streptococcus M-like protein from AP53 bound to human plasminogen | ||||||
Components | M protein (Fragment) | ||||||
Keywords | BLOOD CLOTTING / PAM / human plasminogen / M-protein / Group A streptococcus | ||||||
Function / homology | Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / YSIRK Gram-positive signal peptide / M protein Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Readnour, B.M. / Tjia-Fleck, S.K. / Castellino, F.J. / McCann, N.R. | ||||||
Funding support | United States, 1items
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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, B.M. / Tjia-Fleck, S.K. / McCann, N.R. / Ayinuola, Y.A. / Ploplis, V.A. / Castellino, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tvl.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tvl.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 8tvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/8tvl ftp://data.pdbj.org/pub/pdb/validation_reports/tv/8tvl | HTTPS FTP |
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-Related structure data
Related structure data | 42429MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 40659.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: AP53 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6V4L8 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Plasminogen Binding Group A Streptococcus M-Like Protein from AP53 bound to human plasminogen Type: COMPLEX / Details: PAM was bound to the surface of a lentivirus / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.041 MDa / Experimental value: YES |
Source (natural) | Organism: Streptococcus pyogenes (bacteria) / Strain: AP53 / Cellular location: Cell surface |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293T |
Buffer solution | pH: 7.4 / Details: PBS |
Buffer component | Formula: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Plasminogen binding Group A streptococcus M like protein of AP53 bound to human plasminogen on the surface of a lentivirus |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 109000 X / Nominal defocus max: 34000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4054 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212829 / Num. of class averages: 14 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||
Atomic model building | Details: Phenix map to model / Source name: Other / Type: experimental model |