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Yorodumi- EMDB-16258: Negative stain EM structure of Toxoplasma gondii glideosome-assoc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16258 | ||||||||||||||||||||||||
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Title | Negative stain EM structure of Toxoplasma gondii glideosome-associated connector (subdomain coil 1-3) | ||||||||||||||||||||||||
Map data | conformation 1 | ||||||||||||||||||||||||
Sample |
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Keywords | actin-binding protein / armadillo repeat / solenoid / pleckstrin-homology domain / PROTEIN BINDING | ||||||||||||||||||||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||||||||||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | ||||||||||||||||||||||||
Authors | Chen Q / Rosenthal P | ||||||||||||||||||||||||
Funding support | Finland, Norway, United Kingdom, 7 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16258.map.gz | 7.7 MB | EMDB map data format | |
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Header (meta data) | emd-16258-v30.xml emd-16258.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16258_fsc.xml | 5.3 KB | Display | FSC data file |
Images | emd_16258.png | 21.6 KB | ||
Filedesc metadata | emd-16258.cif.gz | 6.2 KB | ||
Others | emd_16258_additional_1.map.gz emd_16258_additional_2.map.gz emd_16258_half_map_1.map.gz emd_16258_half_map_2.map.gz | 7.7 MB 7.7 MB 14.5 MB 14.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16258 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16258 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16258.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | conformation 1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.3 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: conformation 2
File | emd_16258_additional_1.map | ||||||||||||
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Annotation | conformation 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: conformation 3
File | emd_16258_additional_2.map | ||||||||||||
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Annotation | conformation 3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16258_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16258_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Toxoplasma gondii glideosome-associated connector (coil 1-3)
Entire | Name: Toxoplasma gondii glideosome-associated connector (coil 1-3) |
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Components |
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-Supramolecule #1: Toxoplasma gondii glideosome-associated connector (coil 1-3)
Supramolecule | Name: Toxoplasma gondii glideosome-associated connector (coil 1-3) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Toxoplasma gondii (eukaryote) |
-Macromolecule #1: Toxoplasma gondii glideosome-associated connector (coil 1-3)
Macromolecule | Name: Toxoplasma gondii glideosome-associated connector (coil 1-3) type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Toxoplasma gondii (eukaryote) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | 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 ...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 QPREKTCK DVYDLLNSRV Q QGLSVAIS EVAILQEEVE FLVSQ(MSE)G(MSE)YN QEQLDHQTA(MSE) GADHQYGN(MSE)A FELLAATSAN VKLLQA NEF SK(MSE)ELALIKG QADPEIVLYA VKALTAFCKF PPAAQDTARI QGCPALVTEA CSKINKSGLP NERKEEHLCA RYF LVERTA INRNLYNKTP I(MSE)TELINSWN DYDKGAYTTT LLRFVFRA(MSE)R RVVSDAHVEE LLKANVLQRL IGIISD VNA D(MSE)ALLPDVLF LLGSLAVVPE IKTKIGELNG IAACTDLLQR ALPKPNTAPV VTNVCLAFAN ICIGHKKNTE IFS KLGGPA LNVKVLNDRG HEYDVCNAAS VLLCNLLYKN ES(MSE)KKLLGTN GAPAALVKGL SNYDGSEEKT AIRCLESVFK AISNLSLYT PNIQPFLDAG IENAYSTWLS NLSETFPDAQ LETGCRTLVN LV(MSE)ENEENN(MSE) RKFGVCLLPC (MSE)AVAKQGRT DTKALLLLLD IEASLCRLKE NAEAFAANGG IETTIRLIHQ FDYDVGLLTL GIHLLGIQSA VKDSIQR (MSE)(MSE) DADVFSILVG CVEVDAEGNE VTDLVVGGLR CTRRIVRSEE LAFEYCNAGG IATIANVICK SINQP(MSE) V(MSE)L EACRVLLGLL FYTTRSQADR QAAVEALHAQ CQQRAEQ(MSE)HA QAQADYEAGV VSEPPPEE(MSE)E VPEPD PDEL ANAAYGGWYQ (MSE)G(MSE)DEV(MSE)IDA ILQAVCACAA VEAHAKQLRL QRVCLGLAAY FASEQ(MSE)GTSS LVGSGIEQV LTQI(MSE)TNFAG EGTT(MSE)QLSCV IINSIA(MSE)TSG D(MSE)YEEIKTSA LLSALKTSVG K (MSE)ATKKPEE KALKETCAAT LEAAS |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Staining | Type: NEGATIVE / Material: sodium silicotungstate |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination 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 |