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- PDB-8tvl: Plasminogen binding group A streptococcus M-like protein from AP5... -

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Basic information

Entry
Database: PDB / ID: 8tvl
TitlePlasminogen binding group A streptococcus M-like protein from AP53 bound to human plasminogen
ComponentsM protein (Fragment)
KeywordsBLOOD CLOTTING / PAM / human plasminogen / M-protein / Group A streptococcus
Function / homologyPlasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / YSIRK Gram-positive signal peptide / M protein
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsReadnour, B.M. / Tjia-Fleck, S.K. / Castellino, F.J. / McCann, N.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL013424 United States
CitationJournal: 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
DepositionAug 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references
Category: database_2 / em_db_reference / pdbx_database_related
Item: _database_2.database_code / _em_db_reference.access_code / _pdbx_database_related.db_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M protein (Fragment)


Theoretical massNumber of molelcules
Total (without water)40,6601
Polymers40,6601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein M protein (Fragment)


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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
Molecular weightValue: 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 solutionpH: 7.4 / Details: PBS
Buffer componentFormula: PBS
SpecimenEmbedding 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 supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: 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
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron 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
IDNameVersionCategory
7UCSF ChimeraX1.2model fitting
12cryoSPARC3D reconstruction
13PHENIX15.07model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212829 / Num. of class averages: 14 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: Phenix map to model / Source name: Other / Type: experimental model

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