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- PDB-8tvl: Plasminogen binding group A streptococcus M-like protein from AP5... -
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Open data
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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 | ||||||
![]() | M protein (Fragment) | ||||||
![]() | BLOOD CLOTTING / PAM / human plasminogen / M-protein / Group A streptococcus | ||||||
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![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | Readnour, B.M. / Tjia-Fleck, S.K. / Castellino, F.J. / McCann, N.R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.4 KB | Display | ![]() |
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PDB format | ![]() | 97.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 31.8 KB | Display | |
Data in CIF | ![]() | 43.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 42429MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() |
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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 |
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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: ![]() |
Source (recombinant) | Organism: ![]() |
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 |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / 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 |
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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 |