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- EMDB-16260: Negative stain EM structure of Toxoplasma gondii glideosome-assoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-16260
TitleNegative stain EM structure of Toxoplasma gondii glideosome-associated connector (subdomain coil 1-2)
Map data
Sample
  • Complex: Toxoplasma gondii glideosome-associated connector (coil 1-2)
    • Protein or peptide: Toxoplasma gondii glideosome-associated connector (coil 1-2)
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
Medical Research Council (MRC, United Kingdom)CC2106 United Kingdom
Wellcome TrustCC2106 United Kingdom
Cancer Research UKCC2106 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_16260.png

Downloads & links

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Map

FileDownload / File: emd_16260.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 100 pix.
= 330. Å		3.3 Å/pix.
x 100 pix.
= 330. Å		3.3 Å/pix.
x 100 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.76
Minimum - Maximum-0.2847308 - 7.9756474
Average (Standard dev.)0.028999174 (±0.29209515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16260_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_16260_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 1-2)

EntireName: Toxoplasma gondii glideosome-associated connector (coil 1-2)
Components
  • Complex: Toxoplasma gondii glideosome-associated connector (coil 1-2)
    • Protein or peptide: Toxoplasma gondii glideosome-associated connector (coil 1-2)

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Supramolecule #1: Toxoplasma gondii glideosome-associated connector (coil 1-2)

SupramoleculeName: Toxoplasma gondii glideosome-associated connector (coil 1-2)
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 1-2)

MacromoleculeName: Toxoplasma gondii glideosome-associated connector (coil 1-2)
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KRNPDAGVAT AVQSVIQHQT FKR(MSE)LLFGLR SLADFCSPSN QLYQENALDA LDRGVLSAIQ TAVTT FSDD DDL(MSE)LCASRV LWA(MSE)SVAIKE E(MSE)DPAHIARV HSEGSPVIVA VVNSSPTDPQ TIEDS(MSE)NFVD NLKRAGAPV DGASLAGG(MSE)L ...String:
KRNPDAGVAT AVQSVIQHQT FKR(MSE)LLFGLR SLADFCSPSN QLYQENALDA LDRGVLSAIQ TAVTT FSDD DDL(MSE)LCASRV LWA(MSE)SVAIKE E(MSE)DPAHIARV HSEGSPVIVA VVNSSPTDPQ TIEDS(MSE)NFVD NLKRAGAPV DGASLAGG(MSE)L SIFTKTALD(MSE) KTAKRVTAAL AIAAETAEGS TALYNAGGTS VLLTYCLDQG DLS DAGVE(MSE) VEGAFDTVRY (MSE)AGYQCTDAT TLPQCIAL(MSE)D KYRGRKSASA KGSSALAA(MSE)I GPEQLQKC L NTLKTAEAGS AEYDEALVTL GS(MSE)SYISSFT DEIVRAGGVP LLIELINSGL PQ(MSE)EGNPEKI AS(MSE)ISGA AK (MSE)LARIASNPV NVDAIVQAGG VATLCTAVSY CTES(MSE)EALGA LC(MSE)ALVPLAS RESLAHEIVQ YQTFAT VLP ILYQNVESPE IAALA(MSE)ELVA TGSQHEEIQE H(MSE)LQNQAAEI CSLCCQYHTA DASYQQHAIS ALNRLVPRL TTLHGVSEYG GIQGVIASLN ANVNNEQVAL LAVQLLDNFS EVSDAKTY(MSE)S DGTCVDAVLA A(MSE)LEHEGNDL LI SAGVHCL ARIATEDDCA RHLNVLDTAI QTARGNPDGV YRVLAAISGL SRVPSLRQIF EEKNASDTIL AGISSWIECS RFE GQNRII KAALKTVKN(MSE) KISGDGDLTS CFAA(MSE)CDVAC LPQVKRVVEL EEPDNNILVA DTAAFRDLAA T(MSE) RITGAEN LERCIESVLR V(MSE)RKYPDSRR AQLNCLETLN YLAQCDGGEG VAILSRTGGL NAVVQYLTRA P(MSE)YLD AQIA GFTVLATSAK IDSNVGETLR KCNCLQALKV A(MSE)RTHAKSKE LKRTIAPLVA LL(MSE)PTDALET EIQELLNE C ASACEKNNFP HLHENLAALN ELLISSEGAK IAARLGIGAH (MSE)CKYQEYISA HEQDALAVTD YDILGKDLFD ATVSE CAHA (MSE)EQVASTRSG RNALIKAGNV ATLISLYESL KAPQSQYSEE AAIHCLEALR ILLKSDKRSA ELAFERNFVS TL CVGIDSF PHSAPVLGAT CACLAA(MSE)ATT PERVQ(MSE)LTAQ PAFESLLQKL VFVIQNDPSK DNKLVA(MSE)RAL Q ELVEITND AT(MSE)ANKIAEA GAVTALFRII DEYGDDEQLT VQAAEVLALL GAFEDLRRFY DNDVRFPAQV LTAALTKQ K NNETAVVHLL DVLNKLATSE DRAVLRELGV (MSE)EQVADA(MSE)RV HSESEAVTRL GGELFAK(MSE)GA DEQIKSL (MSE)L QIIETVESGA EDTAQTVDIL CGRLAVFLAA PLEDPRDALQ HTEKCLGSLV ATLQTYPGSE RLEGNVALVC RRLC DRCFD DADDPYGAWA VAASG(MSE)LAQF AG(MSE)VAGETVL ANKKFLGPAY RTFTACCANA YC(MSE)PT(MSE)VEV APSFLPQTYT LLE(MSE)HKNDAE TVARVLEFLR YFAEDPTACG LIVQN(MSE)SGSS GDVVALTVLL (MSE)QQHQNND A VVCAG(MSE)EFLG ALAYTLSQAG YEPLPTLADG SVLRDCDAL(MSE) GSNSSSARQL AH(MSE)H(MSE)IEK(MSE) LLSKAYNDAL IQEQALKKLT (MSE)SLKAEDDKK RFSDEERAGL YAA(MSE)ACVLLA AGGAGLTGE(MSE) EKFNGFEV V LQAIEEFGEN PTVIKEVNRA LQGLS(MSE)ADVN (MSE)TARTVKEAV PKLCTEATTA IQTDAECADT FCDL(MSE)LQ LV SQEGNGRQLL QVYGLEETLQ GVENLAAYYG EDFGTQLSEK VA(MSE)IRQA(MSE)ED D

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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
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37876
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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