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- EMDB-75723: Refined plasminogen binding group A streptococcus M-like protein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-75723
TitleRefined plasminogen binding group A streptococcus M-like protein isolate from AP53 bound to human plasminogen
Map dataFull map of PAM associated to hPg on the surface of a lentivirus
Sample
  • Complex: Plasminogen Binding Group A Streptococcus M-Like Protein from AP53 bound to human plasminogen
    • Protein or peptide: plasminogen binding group A streptococcus M-like protein
KeywordsPAM / human plasminogen / M-protein / Group A streptococcus / BLOOD CLOTTING
Biological speciesStreptococcus pyogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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: Structure / Year: 2024
Title: High-resolution cryo-EM anaylysis of a streptococcus pyogenes M-protein/ plasminogen complex
Authors: Readnour BM / Tjia Fleck S / McCann MR / Ayinuola YA / Castellino FJ
History
DepositionFeb 26, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75723.png

Downloads & links

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Map

FileReleased
AnnotationFull map of PAM associated to hPg on the surface of a lentivirus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.54 Å/pix.
x 300 pix.
= 162. Å		0.54 Å/pix.
x 300 pix.
= 162. Å		0.54 Å/pix.
x 300 pix.
= 162. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028
Minimum - Maximum-0.37731624 - 0.15069166
Average (Standard dev.)0.0006245393 (±0.00864876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 162.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of PAM associated to hPg on the surface of a lentivirus

Fileemd_75723_half_map_1.map
AnnotationHalf map of PAM associated to hPg on the surface of a lentivirus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of PAM associated to hPg on the surface of a lentivirus

Fileemd_75723_half_map_2.map
AnnotationHalf map of PAM associated to hPg on the surface of a lentivirus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
    • Protein or peptide: plasminogen binding group A streptococcus M-like protein

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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: all / 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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Macromolecule #1: plasminogen binding group A streptococcus M-like protein

MacromoleculeName: plasminogen binding group A streptococcus M-like protein
type: protein_or_peptide / ID: 1
Details: Plasminogen binding molecule on the surface of group A streptococcus pyogenes
Enantiomer: DEXTRO
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Recombinant expressionOrganism: Human immunodeficiency virus 2
SequenceString: NRADDARNEV LRGNLVRAEL WYRQIQENDQ LKLENKGLKT DLREKEEELQ GLKDDVEKLT ADAELQRLKN ERHEEAELER LKSERHDHDK KEAERKALED KLADKQEHLN GALRYINEKE AERKEKEAEQ KKLKEEKQIS DASRQGLRRD LDASREAKKQ VEKDLANLTA ...String:
NRADDARNEV LRGNLVRAEL WYRQIQENDQ LKLENKGLKT DLREKEEELQ GLKDDVEKLT ADAELQRLKN ERHEEAELER LKSERHDHDK KEAERKALED KLADKQEHLN GALRYINEKE AERKEKEAEQ KKLKEEKQIS DASRQGLRRD LDASREAKKQ VEKDLANLTA ELDKVKEEKQ ISDASRQGLR RDLDASREAK KQVEKGLANL TAELDKVKEE KQISDASRQG LRRDLDASRE AKKQVEKALE EANSKLAALE KLNKELEESK KLTEKEKAEL QAKLEAEAKA LKEQLAKQAE ELAKLRAEKA SDSQTPDAKP GNKAVPGKGQ APQAGTKPNQ NKAPMKETKR QLPSTG

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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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 212829
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 14 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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