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- EMDB-42429: Plasminogen binding group A streptococcus M-like protein from AP5... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-42429
TitlePlasminogen binding group A streptococcus M-like protein from AP53 bound to human plasminogen
Map dataFull Map of hPg bound to PAM on 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
Function / homology
Function and homology information


plasminogen activation / extracellular region
Similarity search - Function
Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / : / Streptococcal M proteins D repeats region profile. / : / Streptococcal M proteins C repeat profile. / YSIRK Gram-positive signal peptide
Similarity search - Domain/homology
Plasminogen-binding group A streptococcal M-like protein PAM
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsReadnour BM / Tjia-Fleck SK / Castellino FJ / McCann NR
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
DepositionOct 19, 2023-
SupersessionNov 1, 2023ID: EMD-41638
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42429.png

Downloads & links

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Map

FileDownload / File: emd_42429.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull Map of hPg bound to PAM on a lentivirus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.44 Å/pix.
x 360 pix.
= 157.32 Å		0.44 Å/pix.
x 360 pix.
= 157.32 Å		0.44 Å/pix.
x 360 pix.
= 157.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.437 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.08224377 - 0.087504186
Average (Standard dev.)0.00096694287 (±0.0058300225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 157.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map of hPg bound to PAM on a lentivirus

Fileemd_42429_half_map_1.map
AnnotationHalf Map of hPg bound to PAM on a lentivirus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map of hPg bound to PAM on a lentivirus

Fileemd_42429_half_map_2.map
AnnotationHalf Map of hPg bound to PAM on 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 / Enantiomer: DEXTRO
Source (natural)Organism: Streptococcus pyogenes (bacteria) / Strain: AP53
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNRADDARNE VLRGNLVRAE LWYRQIQEND QL KLENKGL KTDLREKEEE LQGLKDDVEK LTADAELQRL KNERHEEAEL ERLKSERHDH DKK EAERKA LEDKLADKQE HLNGALRYIN EKEAEAKEKE AEQKKLKEEK QISDASRQGL RRDL DASRE AKKQVEKDLA ...String:
MNRADDARNE VLRGNLVRAE LWYRQIQEND QL KLENKGL KTDLREKEEE LQGLKDDVEK LTADAELQRL KNERHEEAEL ERLKSERHDH DKK EAERKA LEDKLADKQE HLNGALRYIN EKEAEAKEKE AEQKKLKEEK QISDASRQGL RRDL DASRE AKKQVEKDLA NLTAELDKVK EEKQISDASR QGLRRDLDAS REAKKQVEKG LANLT AELD KVKEEKQISD ASRQGLRRDL DASREAKKQV EKALEEANSK LAALEKLNKE LEESKK LTE KEKAELQAKL EAEAKALKEQ LAKQAEELAK LRAEKASDSQ TPDAKPGNKA VPGKGQA PQ AGTKPNQNKA PMKETKRQLP STG

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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 - Formula: 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: 14 / Resolution.type: BY AUTHOR / Resolution: 4.2 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
Output model

PDB-8tvl:
Plasminogen binding group A streptococcus M-like protein from AP53 bound to human plasminogen

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