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- EMDB-16259: Negative stain EM structure of Toxoplasma gondii glideosome-assoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-16259
TitleNegative stain EM structure of Toxoplasma gondii glideosome-associated connector subdomain coil 3
Map data
Sample
  • Complex: Toxoplasma gondii glideosome-associated connector (coil 3)
    • Protein or peptide: Toxoplasma gondii glideosome-associated connector (coil 3)
Keywordsactin-binding protein / armadillo repeat / solenoid / pleckstrin-homology domain / PROTEIN BINDING
Biological speciesToxoplasma gondii (eukaryote)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsChen Q / Rosenthal P
Funding support Finland, Norway, United Kingdom, 7 items
OrganizationGrant numberCountry
Academy of Finland Finland
Sigrid Juselius Foundation Finland
Jane and Aatos Erkko Foundation Finland
Norwegian Research Council Norway
Cancer Research UKCC2106 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2106 United Kingdom
Wellcome TrustCC2106 United Kingdom
CitationJournal: To Be Published
Title: Structure of Toxoplasma gondii glideosome-associated connector suggests a role as an elastic element to assist myosin A in generating force for gliding motility
Authors: Hung YF / Chen Q / Pires I / Rosenthal P / Kursula I
History
DepositionDec 6, 2022-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16259.png

Downloads & links

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Map

FileDownload / File: emd_16259.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 3.3 Å
Density
Contour LevelBy AUTHOR: 2.9
Minimum - Maximum-0.26914632 - 7.5119796
Average (Standard dev.)0.074879885 (±0.37420574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16259_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16259_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Toxoplasma gondii glideosome-associated connector (coil 3)

EntireName: Toxoplasma gondii glideosome-associated connector (coil 3)
Components
  • Complex: Toxoplasma gondii glideosome-associated connector (coil 3)
    • Protein or peptide: Toxoplasma gondii glideosome-associated connector (coil 3)

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Supramolecule #1: Toxoplasma gondii glideosome-associated connector (coil 3)

SupramoleculeName: Toxoplasma gondii glideosome-associated connector (coil 3)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Toxoplasma gondii (eukaryote)

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Macromolecule #1: Toxoplasma gondii glideosome-associated connector (coil 3)

MacromoleculeName: Toxoplasma gondii glideosome-associated connector (coil 3)
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QPREKTCKDV YDLLNSRVQ QGLSVAISEV AILQEEVEFL VSQ(MSE)G(MSE)YNQE QLDHQTA(MSE)GA DHQYGN(MSE)AFE LLAATSANVK LLQA NEFSK (MSE)ELALIKGQA DPEIVLYAVK ALTAFCKFPP AAQDTARIQG CPALVTEACS KINKSGLPNE ...String:
QPREKTCKDV YDLLNSRVQ QGLSVAISEV AILQEEVEFL VSQ(MSE)G(MSE)YNQE QLDHQTA(MSE)GA DHQYGN(MSE)AFE LLAATSANVK LLQA NEFSK (MSE)ELALIKGQA DPEIVLYAVK ALTAFCKFPP AAQDTARIQG CPALVTEACS KINKSGLPNE RKEEHLCARY F LVERTAIN RNLYNKTPI(MSE) TELINSWNDY DKGAYTTTLL RFVFRA(MSE)RRV VSDAHVEELL KANVLQRLIG IISD VNAD(MSE) ALLPDVLFLL GSLAVVPEIK TKIGELNGIA ACTDLLQRAL PKPNTAPVVT NVCLAFANIC IGHKKNTEIF S KLGGPALN VKVLNDRGHE YDVCNAASVL LCNLLYKNES (MSE)KKLLGTNGA PAALVKGLSN YDGSEEKTAI RCLESVFK A ISNLSLYTPN IQPFLDAGIE NAYSTWLSNL SETFPDAQLE TGCRTLVNLV (MSE)ENEENN(MSE)RK FGVCLLPC (MSE) AVAKQGRTDT KALLLLLDIE ASLCRLKENA EAFAANGGIE TTIRLIHQFD YDVGLLTLGI HLLGIQSAVK DSIQR (MSE)(MSE)DA DVFSILVGCV EVDAEGNEVT DLVVGGLRCT RRIVRSEELA FEYCNAGGIA TIANVICKSI NQP(MSE) V(MSE)LEA CRVLLGLLFY TTRSQADRQA AVEALHAQCQ QRAEQ(MSE)HAQA QADYEAGVVS EPPPEE(MSE)EVP EPD PDELAN AAYGGWYQ(MSE)G (MSE)DEV(MSE)IDAIL QAVCACAAVE AHAKQLRLQR VCLGLAAYFA SEQ(MSE)GTSS L VGSGIEQVLT QI(MSE)TNFAGEG TT(MSE)QLSCVII NSIA(MSE)TSGD(MSE) YEEIKTSALL SALKTSVGK (MSE)ATKKPEEKA LKETCAATLE AAS

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: sodium silicotungstate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8bt6

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11929
FSC plot (resolution estimation)

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