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- EMDB-47001: Streptoccocal alpha enolase embedded in DOPG lipid vesicle -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47001
TitleStreptoccocal alpha enolase embedded in DOPG lipid vesicle
Map dataStreptococcal alpha enolase on lipid DOPG vesicle
Sample
  • Complex: Streptococcal surface enolase major interface embedded into the surface of a lipid vesicle
KeywordsGlycolysis / plasminogen binder / membrane protein / LYASE
Biological speciesStreptococcus pyogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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
DepositionSep 13, 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_47001.png

Downloads & links

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Map

FileDownload / File: emd_47001.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStreptococcal alpha enolase on lipid DOPG vesicle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 256 pix.
= 330.372 Å		1.29 Å/pix.
x 256 pix.
= 330.372 Å		1.29 Å/pix.
x 256 pix.
= 330.372 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.29052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.32
Minimum - Maximum-25.748149999999999 - 32.762650000000001
Average (Standard dev.)0.0006325699 (±1.0709019)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1-1-1
Dimensions256256256
Spacing256256256
CellA=B=C: 330.372 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Streptococcal surface enolase major interface embedded into the s...

EntireName: Streptococcal surface enolase major interface embedded into the surface of a lipid vesicle
Components
  • Complex: Streptococcal surface enolase major interface embedded into the surface of a lipid vesicle

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Supramolecule #1: Streptococcal surface enolase major interface embedded into the s...

SupramoleculeName: Streptococcal surface enolase major interface embedded into the surface of a lipid vesicle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 95 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
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) / 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 / Cs: 2.7 mm / Nominal defocus max: 29.0 µm / Nominal defocus min: 1.0 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: 3300000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ugu

Final reconstructionNumber classes used: 7 / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX (ver. 1.2.5) / Number images used: 414427
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 7

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