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- EMDB-42462: Human Plasminogen bound to streptococcal surface enolase -

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Basic information

Entry
Database: EMDB / ID: EMD-42462
TitleHuman Plasminogen bound to streptococcal surface enolase
Map dataMain map of human plasminogen bound to SEN on the surface of a lipid
Sample
  • Complex: Human plasminogen bound to streptococcal enolase on the surface of a lipid vesicle
    • Protein or peptide: Plasminogen
KeywordsGlycolysis / plasminogen binder / membrane protein / LYASE
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / Schaffer collateral - CA1 synapse / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / endopeptidase activity / protease binding / blood microparticle / negative regulation of cell population proliferation / protein domain specific binding / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. ...Peptidase S1A, plasmin / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsTjia-Fleck S / Readnour BM / Castellino FJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL013423 United States
CitationJournal: To Be Published
Title: Streptococcus surface alpha enolase exposed dimers were found to be the active form on lipid surface that binds to human plasminogen
Authors: Tjia-Fleck S / Readnour BM / Castellino FJ
History
DepositionOct 23, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42462.png

Downloads & links

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Map

FileDownload / File: emd_42462.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map of human plasminogen bound to SEN on the surface of a lipid
Voxel sizeX=Y=Z: 0.539 Å
Density
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.095187455 - 0.06657795
Average (Standard dev.)0.00033086995 (±0.004134603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 181.10399 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A of human plasminogen bound to...

Fileemd_42462_half_map_1.map
Annotationhalf map A of human plasminogen bound to SEN on the surface of a lipid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B of human plasminogen bound to...

Fileemd_42462_half_map_2.map
Annotationhalf map B of human plasminogen bound to SEN on the surface of a lipid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human plasminogen bound to streptococcal enolase on the surface o...

EntireName: Human plasminogen bound to streptococcal enolase on the surface of a lipid vesicle
Components
  • Complex: Human plasminogen bound to streptococcal enolase on the surface of a lipid vesicle
    • Protein or peptide: Plasminogen

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Supramolecule #1: Human plasminogen bound to streptococcal enolase on the surface o...

SupramoleculeName: Human plasminogen bound to streptococcal enolase on the surface of a lipid vesicle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91 KDa

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Macromolecule #1: Plasminogen

MacromoleculeName: Plasminogen / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.544461 KDa
Recombinant expressionOrganism: Drosophila (fruit flies)
SequenceString: EPLDDYVNTQ GASLFSVTKK QLGAGSIEEC AAKCEEDEEF TCRAFQYHSK EQQCVIMAEN RKSSIIIRMR DVVLFEKKVY LSECKTGNG KNYRGTMSKT KNGITCQKWS STSPHRPRFS PATHPSEGLE ENYCRNPDND PQGPWCYTTD PEKRYDYCDI L ECEEECMH ...String:
EPLDDYVNTQ GASLFSVTKK QLGAGSIEEC AAKCEEDEEF TCRAFQYHSK EQQCVIMAEN RKSSIIIRMR DVVLFEKKVY LSECKTGNG KNYRGTMSKT KNGITCQKWS STSPHRPRFS PATHPSEGLE ENYCRNPDND PQGPWCYTTD PEKRYDYCDI L ECEEECMH CSGENYDGKI SKTMSGLECQ AWDSQSPHAH GYIPSKFPNK NLKKNYCRNP DRELRPWCFT TDPNKRWELC DI PRCTTPP PSSGPTYQCL KGTGENYRGN VAVTVSGHTC QHWSAQTPHT HNRTPENFPC KNLDENYCRN PDGKRAPWCH TTN SQVRWE YCKIPSCDSS PVSTEQLAPT APPELTPVVQ DCYHGDGQSY RGTSSTTTTG KKCQSWSSMT PHRHQKTPEN YPNA GLTMN YCRNPDADKG PWCFTTDPSV RWEYCNLKKC SGTEASVVAP PPVVLLPDVE TPSEEDCMFG NGKGYRGKRA TTVTG TPCQ DWAAQEPHRH SIFTPETNPR AGLEKNYCRN PDGDVGGPWC YTTNPRKLYD YCDVPQCAAP SFDCGKPQVE PKKCPG RVV GGCVAHPHSW PWQVSLRTRF GMHFCGGTLI SPEWVLTAAH CLEKSPRPSS YKVILGAHQE VNLEPHVQEI EVSRLFL EP TRKDIALLKL SSPAVITDKV IPACLPSPNY VVADRTECFI TGWGETQGTF GAGLLKEAQL PVIENKVCNR YEFLNGRV Q STELCAGHLA GGTDSCQGDS GGPLVCFEKD KYILQGVTSW GLGCARPNKP GVYVRVSRFV TWIEGVMRNN

UniProtKB: Plasminogen

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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
GridModel: C-flat-1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4776 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 2500000
Startup modelType of model: NONE
Final reconstructionNumber classes used: 14 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1024556
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 14 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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