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- EMDB-46967: Refined plasminogen binding group A streptococcus M-like protein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-46967
TitleRefined plasminogen binding group A streptococcus M-like protein isolate from AP53 bound to human plasminogen full map
Map dataRefined PAM isolate from EMD-42429 map.
Sample
  • Complex: Plasminogen Binding Group A Streptococcus M-Like Protein from AP53 bound to human plasminogen
KeywordsPAM / human plasminogen / M-protein / Group A streptococcus / BLOOD CLOTTING
Biological speciesStreptococcus pyogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsReadnour BM / Tjia-Fleck SK / Castellino FJ
Funding support United States, 1 items
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 BM / Tjia-Fleck SK / McCann NR / Ayinuola YA / Ploplis VA / Castellino FJ
History
DepositionSep 9, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46967.png

Downloads & links

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Map

FileDownload / File: emd_46967.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined PAM isolate from EMD-42429 map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.8 Å/pix.
x 360 pix.
= 1368. Å		3.8 Å/pix.
x 360 pix.
= 1368. Å		3.8 Å/pix.
x 360 pix.
= 1368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.22
Minimum - Maximum-14.081867000000001 - 15.476846
Average (Standard dev.)-0.012572726 (±0.73909646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 1368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Plasminogen Binding Group A Streptococcus M-Like Protein from AP5...

EntireName: Plasminogen Binding Group A Streptococcus M-Like Protein from AP53 bound to human plasminogen
Components
  • Complex: Plasminogen Binding Group A Streptococcus M-Like Protein from AP53 bound to human plasminogen

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Supramolecule #1: Plasminogen Binding Group A Streptococcus M-Like Protein from AP5...

SupramoleculeName: Plasminogen Binding Group A Streptococcus M-Like Protein from AP53 bound to human plasminogen
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: PAM was bound to the surface of a lentivirus
Source (natural)Organism: Streptococcus pyogenes (bacteria) / Strain: AP53 / Location in cell: Cell surface
Molecular weightTheoretical: 41 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 1.0 X / Component - Formula: PBS / Component - Name: PBS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsPlasminogen binding Group A streptococcus M like protein of AP53 bound to human plasminogen on the surface of a lentivirus

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 4054 / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 124 / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212829
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 14
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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