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- EMDB-42435: Major interface of Streptococcal surface enolase dimer from AP53 ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-42435
TitleMajor interface of Streptococcal surface enolase dimer from AP53 group A streptococcus bound to a lipid vesicle
Map dataSEN dimer map on the surface of lipid major dimer interface
Sample
  • Complex: Streptococcal surface enolase major interface embedded into the surface of a lipid vesicle
    • Protein or peptide: Enolase
KeywordsGlycolysis / plasminogen binder / membrane protein / LYASE
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / peptidoglycan-based cell wall / glycolytic process / magnesium ion binding / cell surface / extracellular region
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily
Similarity search - Domain/homology
Biological speciesStreptococcus pyogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 20, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42435.png

Downloads & links

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Map

FileDownload / File: emd_42435.map.gz / Format: CCP4 / Size: 37.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSEN dimer map on the surface of lipid major dimer interface
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 214 pix.
= 230.692 Å		1.08 Å/pix.
x 214 pix.
= 230.692 Å		1.08 Å/pix.
x 214 pix.
= 230.692 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0678
Minimum - Maximum-1.7132988 - 1.7777559
Average (Standard dev.)-0.00038992535 (±0.021561516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions214214214
Spacing214214214
CellA=B=C: 230.69199 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: SEN dimer map on the surface of lipid combined dimer interfaces

Fileemd_42435_additional_1.map
AnnotationSEN dimer map on the surface of lipid combined dimer interfaces
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SEN dimer half map on the surface of lipid major dimer interface B

Fileemd_42435_half_map_1.map
AnnotationSEN dimer half map on the surface of lipid major dimer interface B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SEN dimer half map on the surface of lipid major dimer interface A

Fileemd_42435_half_map_2.map
AnnotationSEN dimer half map on the surface of lipid major dimer interface A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
    • Protein or peptide: Enolase

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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: all
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 95 KDa

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Macromolecule #1: Enolase

MacromoleculeName: Enolase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: phosphopyruvate hydratase
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 47.543281 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: HMSIITDVYA REVLDSRGNP TLEVEVYTES GAFGRGMVPS GASTGEHEAV ELRDGDKSRY LGLGTQKAVD NVNNIIAEAI IGYDVRDQQ AIDRAMIALD GTPNKGKLGA NAILGVSIAV ARAAADYLEV PLYTYLGGFN TKVLPTPMMN IINGGSHSDA P IAFQEFMI ...String:
HMSIITDVYA REVLDSRGNP TLEVEVYTES GAFGRGMVPS GASTGEHEAV ELRDGDKSRY LGLGTQKAVD NVNNIIAEAI IGYDVRDQQ AIDRAMIALD GTPNKGKLGA NAILGVSIAV ARAAADYLEV PLYTYLGGFN TKVLPTPMMN IINGGSHSDA P IAFQEFMI MPVGAPTFKE GLRWGAEVFH ALKKILKERG LVTAVGDEGG FAPKFEGTED GVETILKAIE AAGYEAGENG IM IGFDCAS SEFYDKERKV YDYTKFEGEG AAVRTSAEQV DYLEELVNKY PIITIEDGMD ENDWDGWKVL TERLGKRVQL VGD DFFVTN TEYLARGIKE NAANSILIKV NQIGTLTETF EAIEMAKEAG YTAVVSHRSG ETEDSTIADI AVATNAGQIK TGSL SRTDR IAKYNQLLRI EDQLGEVAQY KGIKSFYNLK K

UniProtKB: Enolase

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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
GridMaterial: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX / Number images used: 525846
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 7
FSC plot (resolution estimation)

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