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- EMDB-23869: Cryo-EM structure of cortical microtubule from Toxoplasma gondii ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23869 | |||||||||
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Title | Cryo-EM structure of cortical microtubule from Toxoplasma gondii (with TrxL2) | |||||||||
![]() | Composite map of T. gondii cortical microtubule (with TrxL2) | |||||||||
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Function / homology | ![]() microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Wang X / Brown A / Sibley LD / Zhang R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of cortical microtubules from human parasite Toxoplasma gondii identifies their microtubule inner proteins. Authors: Xiangli Wang / Yong Fu / Wandy L Beatty / Meisheng Ma / Alan Brown / L David Sibley / Rui Zhang / ![]() Abstract: In living cells, microtubules (MTs) play pleiotropic roles, which require very different mechanical properties. Unlike the dynamic MTs found in the cytoplasm of metazoan cells, the specialized ...In living cells, microtubules (MTs) play pleiotropic roles, which require very different mechanical properties. Unlike the dynamic MTs found in the cytoplasm of metazoan cells, the specialized cortical MTs from Toxoplasma gondii, a prevalent human pathogen, are extraordinarily stable and resistant to detergent and cold treatments. Using single-particle cryo-EM, we determine their ex vivo structure and identify three proteins (TrxL1, TrxL2 and SPM1) as bona fide microtubule inner proteins (MIPs). These three MIPs form a mesh on the luminal surface and simultaneously stabilize the tubulin lattice in both longitudinal and lateral directions. Consistent with previous observations, deletion of the identified MIPs compromises MT stability and integrity under challenges by chemical treatments. We also visualize a small molecule like density at the Taxol-binding site of β-tubulin. Our results provide the structural basis to understand the stability of cortical MTs and suggest an evolutionarily conserved mechanism of MT stabilization from the inside. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 64.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.6 KB 25.6 KB | Display Display | ![]() |
Images | ![]() | 145.9 KB | ||
Others | ![]() ![]() | 49.9 MB 229.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 449.5 KB | Display | ![]() |
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Full document | ![]() | 449.1 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mizMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Composite map of T. gondii cortical microtubule (with TrxL2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.096 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened composite map of T. gondii cortical microtubule...
File | emd_23869_additional_1.map | ||||||||||||
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Annotation | Unsharpened composite map of T. gondii cortical microtubule (with TrxL2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: B-factor sharpened composite map of T. gondii cortical...
File | emd_23869_additional_2.map | ||||||||||||
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Annotation | B-factor sharpened composite map of T. gondii cortical microtubule (with TrxL2) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : cortical microtubule with associated MIPs
Entire | Name: cortical microtubule with associated MIPs |
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Components |
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-Supramolecule #1: cortical microtubule with associated MIPs
Supramolecule | Name: cortical microtubule with associated MIPs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Microtubule associated protein SPM1
Macromolecule | Name: Microtubule associated protein SPM1 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 38.84575 KDa |
Sequence | String: MSGGNSNTPK KLPSEEGSDY GYPQKPQKYL PKSEQAEPDY SACCKGNDAY KGASHGTVQF SHPEEAQKYA GAAAGAETIQ RGRERVAAD RQPRAAGDVP ARRLHLSDVD EAHRGQSPSR HPGYCVEELC TCGMHKCIPS RAPVPFTGST QYRQEFVPKP L PPPTQVSQ ...String: MSGGNSNTPK KLPSEEGSDY GYPQKPQKYL PKSEQAEPDY SACCKGNDAY KGASHGTVQF SHPEEAQKYA GAAAGAETIQ RGRERVAAD RQPRAAGDVP ARRLHLSDVD EAHRGQSPSR HPGYCVEELC TCGMHKCIPS RAPVPFTGST QYRQEFVPKP L PPPTQVSQ VTLPPSLPFE AESSYRTEFV AKPLPPPAKF SEVKLPPTLP FHGESAYRTD YVPKPLPEVA KPVEVKLPPT LP FNAQSCY RSEYVAKPLP PPVQTVEVKL PPSLPFEGST HYRDEFQVKP LPPATKVTEV KLPPSLPFDA TSMYRSDYVA KSN PICPVS KLPQYPAATY PQNHVFWDPD TKQWY |
-Macromolecule #2: Tubulin alpha chain
Macromolecule | Name: Tubulin alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 50.166645 KDa |
Sequence | String: MREVISIHVG QAGIQIGNAC WELFCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCVFLDL EPTVVDEVRT GTYRHLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLSL DRIRKLADNC TGLQGFLMFN AVGGGTGSGL GCLLLERLSV D YGKKSKLN ...String: MREVISIHVG QAGIQIGNAC WELFCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCVFLDL EPTVVDEVRT GTYRHLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLSL DRIRKLADNC TGLQGFLMFN AVGGGTGSGL GCLLLERLSV D YGKKSKLN FCSWPSPQVS TAVVEPYNSV LSTHSLLEHT DVAVMLDNEA IYDICRRNLD IERPTYTNLN RLIAQVISSL TA SLRFDGA LNVDVTEFQT NLVPYPRIHF MLSSYAPIIS AEKAYHEQLS VAEITNSAFE PASMMAKCDP RHGKYMACCL MYR GDVVPK DVNAAVATIK TKRTIQFVDW CPTGFKCGIN YQPPTVVPGG DLAKVMRAVC MISNSTAIAE VFSRMDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDYEEV GIETAEGEGE EEGYGDEY |
-Macromolecule #3: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 50.119121 KDa |
Sequence | String: MREIVHVQGG QCGNQIGAKF WEVISDEHGI DPTGTYCGDS DLQLERINVF YNEATGGRFV PRAILMDLEP GTMDSVRAGP FGQLFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAEGCDC LQGFQITHSL GGGTGSGMGT LLISKVREEY P DRIMETFS ...String: MREIVHVQGG QCGNQIGAKF WEVISDEHGI DPTGTYCGDS DLQLERINVF YNEATGGRFV PRAILMDLEP GTMDSVRAGP FGQLFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAEGCDC LQGFQITHSL GGGTGSGMGT LLISKVREEY P DRIMETFS VFPSPKVSDT VVEPYNATLS VHQLVENADE VQVIDNEALY DICFRTLKLT TPTYGDLNHL VSAAMSGVTC CL RFPGQLN SDLRKLAVNL IPFPRLHFFL IGFAPLTSRG SQQYRALSVP ELTQQMFDAK NMMCASDPRH GRYLTASAMF RGR MSTKEV DEQMLNVQNK NSSYFVEWIP NNMKSSVCDI PPKGLKMSVT FVGNSTAIQE MFKRVSDQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEGE FDEEEGEMGA EEGA |
-Macromolecule #4: PDI family protein
Macromolecule | Name: PDI family protein / type: protein_or_peptide / ID: 4 / Number of copies: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.939332 KDa |
Sequence | String: MSQPVFASPL NVEKRRLNEE RALMQAQKAG GEGVNIQLPP NYGDMDLILF PEGSLKNSNN TVIPQSHLKG KSVALYFADG ADPKCASLL PFLLNYYRTM NEGGANQKIE IIFVSLDRDR EAFESHRAHM PWLSIDLENP LTEILKRHFR VMKEYEVPTY G YGSRTGVP ...String: MSQPVFASPL NVEKRRLNEE RALMQAQKAG GEGVNIQLPP NYGDMDLILF PEGSLKNSNN TVIPQSHLKG KSVALYFADG ADPKCASLL PFLLNYYRTM NEGGANQKIE IIFVSLDRDR EAFESHRAHM PWLSIDLENP LTEILKRHFR VMKEYEVPTY G YGSRTGVP SVIVIGSDGR EAQFLPICSG LEEGDRALLR WDWRNTKFAS DQFHVRPTLL EQ |
-Macromolecule #5: PDI family protein
Macromolecule | Name: PDI family protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.687934 KDa |
Sequence | String: MLAADCFFGP DVVKRTQQGN YVPVRPDHFA GVSVALFFAK AGHSKCAQIV PVVRQFYKTT NFSGEKAVIE IIYVSLDKDE QDFERVRAL MPWCSVEYKS CLRKKLIERY RVPNGELAFG TVRIPSTAIP LLIVIGPNGE EAGRMNFQQS DEFVLQRWDY R FNKWPGSA QRLRTLNDAT DPWKKRLPQN V |
-Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 26 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-Macromolecule #7: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 26 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #8: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 26 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ![]() ChemComp-GDP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds with a blot force of -15. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 2 / Number real images: 9231 / Average exposure time: 9.0 sec. / Average electron dose: 63.7 e/Å2 Details: Images were collected in counting mode, with an exposure rate of 8.5 electrons/pixel/s on the detector camera. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen 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
-Atomic model buiding 1
Initial model | (PDB ID: , , ) |
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Details | Secondary structure, Ramachandran, and rotamer restraints were applied during refinement. The nonbonded_weight value was set to 500 to reduce the clashes between atoms. |
Refinement | Protocol: AB INITIO MODEL |
Output model | ![]() PDB-7miz: |