+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-7101 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | TPX2_mini decorated GMPCPP-microtubule | ||||||||||||||||||
![]() | TPX2_mini decorated GMPCPP- microtubule | ||||||||||||||||||
![]() |
| ||||||||||||||||||
![]() | mitosis / GanGTP / nucleation / CELL CYCLE | ||||||||||||||||||
Function / homology | ![]() nuclear microtubule / microtubule nucleation / axon hillock / importin-alpha family protein binding / negative regulation of microtubule depolymerization / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic ...nuclear microtubule / microtubule nucleation / axon hillock / importin-alpha family protein binding / negative regulation of microtubule depolymerization / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / intercellular bridge / activation of protein kinase activity / protein kinase activator activity / mitotic spindle assembly / regulation of mitotic spindle organization / AURKA Activation by TPX2 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / mitotic spindle / spindle pole / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / Regulation of TP53 Activity through Phosphorylation / molecular adaptor activity / cell division / GTPase activity / apoptotic process / GTP binding / protein kinase binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||
![]() | Zhang R / Nogales E | ||||||||||||||||||
Funding support | ![]() ![]()
| ||||||||||||||||||
![]() | ![]() Title: Structural insight into TPX2-stimulated microtubule assembly. Authors: Rui Zhang / Johanna Roostalu / Thomas Surrey / Eva Nogales / ![]() ![]() Abstract: During mitosis and meiosis, microtubule (MT) assembly is locally upregulated by the chromatin-dependent Ran-GTP pathway. One of its key targets is the MT-associated spindle assembly factor TPX2. The ...During mitosis and meiosis, microtubule (MT) assembly is locally upregulated by the chromatin-dependent Ran-GTP pathway. One of its key targets is the MT-associated spindle assembly factor TPX2. The molecular mechanism of how TPX2 stimulates MT assembly remains unknown because structural information about the interaction of TPX2 with MTs is lacking. Here, we determine the cryo-electron microscopy structure of a central region of TPX2 bound to the MT surface. TPX2 uses two flexibly linked elements ('ridge' and 'wedge') in a novel interaction mode to simultaneously bind across longitudinal and lateral tubulin interfaces. These MT-interacting elements overlap with the binding site of importins on TPX2. Fluorescence microscopy-based in vitro reconstitution assays reveal that this interaction mode is critical for MT binding and facilitates MT nucleation. Together, our results suggest a molecular mechanism of how the Ran-GTP gradient can regulate TPX2-dependent MT formation. | ||||||||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 155.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 17 KB 17 KB | Display Display | ![]() |
Images | ![]() | 408.4 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 525.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 525.2 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bjcMC ![]() 7102C C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TPX2_mini decorated GMPCPP- microtubule | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : TPX2_mini decorated GMPCPP-microtubule
Entire | Name: TPX2_mini decorated GMPCPP-microtubule |
---|---|
Components |
|
-Supramolecule #1: TPX2_mini decorated GMPCPP-microtubule
Supramolecule | Name: TPX2_mini decorated GMPCPP-microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|
-Supramolecule #2: Tubulin
Supramolecule | Name: Tubulin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Targeting protein for Xklp2
Supramolecule | Name: Targeting protein for Xklp2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
---|---|
Source (natural) | Organism: ![]() |
-Macromolecule #1: Tubulin alpha-1B chain
Macromolecule | Name: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 50.204445 KDa |
Sequence | String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY UniProtKB: Tubulin alpha-1B chain |
-Macromolecule #2: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 49.90777 KDa |
Sequence | String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA UniProtKB: Tubulin beta chain |
-Macromolecule #3: Targeting protein for Xklp2
Macromolecule | Name: Targeting protein for Xklp2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 85.811328 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSQVKSSYSY DAPSDFINFS SLDDEGDTQN IDSWFEEKAN LENKLLGKNG TGGLFQGKTP LRKANLQQAI VTPLKPVDNT YYKEAEKEN LVEQSIPSNA CSSLEVEAAI SRKTPAQPQR RSLRLSAQKD LEQKEKHHVK MKAKRCATPV IIDEILPSKK M KVSNNKKK ...String: MSQVKSSYSY DAPSDFINFS SLDDEGDTQN IDSWFEEKAN LENKLLGKNG TGGLFQGKTP LRKANLQQAI VTPLKPVDNT YYKEAEKEN LVEQSIPSNA CSSLEVEAAI SRKTPAQPQR RSLRLSAQKD LEQKEKHHVK MKAKRCATPV IIDEILPSKK M KVSNNKKK PEEEGSAHQD TAEKNASSPE KAKGRHTVPC MPPAKQKFLK STEEQELEKS MKMQQEVVEM RKKNEEFKKL AL AGIGQPV KKSVSQVTKS VDFHFRTDER IKQHPKNQEE YKEVNFTSEL RKHPSSPARV TKGCTIVKPF NLSQGKKRTF DET VSTYVP LAQQVEDFHK RTPNRYHLRS KKDDINLLPS KSSVTKICRD PQTPVLQTKH RARAVTCKST AELEAEELEK LQQY KFKAR ELDPRILEGG PILPKKPPVK PPTEPIGFDL EIEKRIQERE SKKKTEDEHF EFHSRPCPTK ILEDVVGVPE KKVLP ITVP KSPAFALKNR IRMPTKEDEE EDEPVVIKAQ PVPHYGVPFK PQIPEARTVE ICPFSFDSRD KERQLQKEKK IKELQK GEV PKFKALPLPH FDTINLPEKK VKNVTQIEPF CLETDRRGAL KAQTWKHQLE EELRQQKEAA CFKARPNTVI SQEPFVP KK EKKSVAEGLS GSLVQEPFQL ATEKRAKERQ ELEKRMAEVE AQKAQQLEEA RLQEEEQKKE ELARLRRELV HKANPIRK Y QGLEIKSSDQ PLTVPVSPKF STRFHC UniProtKB: Targeting protein for Xklp2 |
-Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: GTP |
---|---|
Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 12 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Macromolecule | Name: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 6 / Number of copies: 6 / Formula: G2P |
---|---|
Molecular weight | Theoretical: 521.208 Da |
Chemical component information | ![]() ChemComp-G2P: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | helical reconstruction |
Aggregation state | helical array |
-
Sample preparation
Buffer | pH: 6.8 / Details: BRB80 |
---|---|
Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK II / Details: blot for 4 seconds before plunging. |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 4 / Number real images: 2000 / Average exposure time: 6.0 sec. / Average electron dose: 27.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 9.03 Å Applied symmetry - Helical parameters - Δ&Phi: -25.74 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 85000 |
---|---|
Startup model | Type of model: EMDB MAP |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: FREALIGN |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
---|---|
Output model | ![]() PDB-6bjc: |