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- PDB-6bjc: TPX2_mini decorated GMPCPP-microtubule -

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Basic information

Entry
Database: PDB / ID: 6bjc
TitleTPX2_mini decorated GMPCPP-microtubule
Components
  • Targeting protein for Xklp2
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / mitosis / GanGTP / nucleation
Function / homology
Function and homology information


activation of protein kinase activity / negative regulation of microtubule depolymerization / axon hillock / importin-alpha family protein binding / microtubule nucleation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cargo trafficking to the periciliary membrane / Intraflagellar transport ...activation of protein kinase activity / negative regulation of microtubule depolymerization / axon hillock / importin-alpha family protein binding / microtubule nucleation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cargo trafficking to the periciliary membrane / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / intercellular bridge / mitotic spindle assembly / protein serine/threonine kinase activator activity / AURKA Activation by TPX2 / regulation of mitotic spindle organization / neuron migration / microtubule cytoskeleton organization / mitotic spindle / spindle / structural constituent of cytoskeleton / spindle pole / microtubule cytoskeleton / neuron differentiation / mitotic cell cycle / Regulation of TP53 Activity through Phosphorylation / molecular adaptor activity / microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cell division / apoptotic process / GTPase activity / protein kinase binding / GTP binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
TPX2 / Aurora-A binding / TPX2, C-terminal / TPX2 central domain / Targeting protein for Xklp2 (TPX2) domain / Aurora-A binding / Cell cycle regulated microtubule associated protein / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain ...TPX2 / Aurora-A binding / TPX2, C-terminal / TPX2 central domain / Targeting protein for Xklp2 (TPX2) domain / Aurora-A binding / Cell cycle regulated microtubule associated protein / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha-1B chain / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang, R. / Nogales, E.
Funding support United States, United Kingdom, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM051487 United States
Howard Hughes Medical Institute (HHMI) United States
Cancer Research UKFC001163 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001163 United Kingdom
Wellcome TrustFC001163 United Kingdom
CitationJournal: Elife / Year: 2017
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
DepositionNov 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Other / Refinement description / Category: cell / refine
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / cell / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
T: Targeting protein for Xklp2
E: Tubulin alpha-1B chain
F: Tubulin beta chain
J: Tubulin alpha-1B chain
H: Tubulin beta chain
L: Tubulin alpha-1B chain
G: Tubulin beta chain
K: Tubulin alpha-1B chain
I: Tubulin beta chain
P: Targeting protein for Xklp2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)778,85438
Polymers772,29614
Non-polymers6,55824
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56120 Å2
ΔGint-363 kcal/mol
Surface area170700 Å2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21C
12A
22E
13A
23J
14A
24L
15A
25K
16B
26D
17B
27F
18B
28H
19B
29G
110B
210I
111C
211E
112C
212J
113C
213L
114C
214K
115D
215F
116D
216H
117D
217G
118D
218I
119T
219P
120E
220J
121E
221L
122E
222K
123F
223H
124F
224G
125F
225I
126J
226L
127J
227K
128H
228G
129H
229I
130L
230K
131G
231I

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETSERSERAA1 - 4391 - 439
21METMETSERSERCC1 - 4391 - 439
12METMETSERSERAA1 - 4391 - 439
22METMETSERSEREF1 - 4391 - 439
13METMETSERSERAA1 - 4391 - 439
23METMETSERSERJH1 - 4391 - 439
14METMETSERSERAA1 - 4391 - 439
24METMETSERSERLJ1 - 4391 - 439
15METMETSERSERAA1 - 4391 - 439
25METMETSERSERKL1 - 4391 - 439
16METMETASPASPBB1 - 4271 - 417
26METMETASPASPDD1 - 4271 - 417
17METMETASPASPBB1 - 4271 - 417
27METMETASPASPFG1 - 4271 - 417
18METMETASPASPBB1 - 4271 - 417
28METMETASPASPHI1 - 4271 - 417
19METMETASPASPBB1 - 4271 - 417
29METMETASPASPGK1 - 4271 - 417
110METMETASPASPBB1 - 4271 - 417
210METMETASPASPIM1 - 4271 - 417
111METMETSERSERCC1 - 4391 - 439
211METMETSERSEREF1 - 4391 - 439
112METMETSERSERCC1 - 4391 - 439
212METMETSERSERJH1 - 4391 - 439
113METMETSERSERCC1 - 4391 - 439
213METMETSERSERLJ1 - 4391 - 439
114METMETSERSERCC1 - 4391 - 439
214METMETSERSERKL1 - 4391 - 439
115METMETASPASPDD1 - 4271 - 417
215METMETASPASPFG1 - 4271 - 417
116METMETASPASPDD1 - 4271 - 417
216METMETASPASPHI1 - 4271 - 417
117METMETASPASPDD1 - 4271 - 417
217METMETASPASPGK1 - 4271 - 417
118METMETASPASPDD1 - 4271 - 417
218METMETASPASPIM1 - 4271 - 417
119GLYGLYARGARGTE300 - 341300 - 341
219GLYGLYARGARGPN300 - 341300 - 341
120METMETSERSEREF1 - 4391 - 439
220METMETSERSERJH1 - 4391 - 439
121METMETSERSEREF1 - 4391 - 439
221METMETSERSERLJ1 - 4391 - 439
122METMETSERSEREF1 - 4391 - 439
222METMETSERSERKL1 - 4391 - 439
123METMETASPASPFG1 - 4271 - 417
223METMETASPASPHI1 - 4271 - 417
124METMETASPASPFG1 - 4271 - 417
224METMETASPASPGK1 - 4271 - 417
125METMETASPASPFG1 - 4271 - 417
225METMETASPASPIM1 - 4271 - 417
126METMETSERSERJH1 - 4391 - 439
226METMETSERSERLJ1 - 4391 - 439
127METMETSERSERJH1 - 4391 - 439
227METMETSERSERKL1 - 4391 - 439
128METMETASPASPHI1 - 4271 - 417
228METMETASPASPGK1 - 4271 - 417
129METMETASPASPHI1 - 4271 - 417
229METMETASPASPIM1 - 4271 - 417
130METMETSERSERLJ1 - 4391 - 439
230METMETSERSERKL1 - 4391 - 439
131METMETASPASPGK1 - 4271 - 417
231METMETASPASPIM1 - 4271 - 417

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31

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Components

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Protein , 3 types, 14 molecules ACEJLKBDFHGITP

#1: Protein
Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: Q2XVP4
#2: Protein
Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: P02554
#3: Protein Targeting protein for Xklp2 / Differentially expressed in cancerous and non-cancerous lung cells 2 / DIL-2 / Hepatocellular ...Differentially expressed in cancerous and non-cancerous lung cells 2 / DIL-2 / Hepatocellular carcinoma-associated antigen 519 / Hepatocellular carcinoma-associated antigen 90 / Protein fls353 / Restricted expression proliferation-associated protein 100 / p100


Mass: 85811.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPX2, C20orf1, C20orf2, DIL2, HCA519
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
Strain (production host): sf21 / References: UniProt: Q9ULW0

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Non-polymers , 3 types, 24 molecules

#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1TPX2_mini decorated GMPCPP-microtubuleCOMPLEX#1-#30MULTIPLE SOURCES
2TubulinCOMPLEX#1-#21NATURAL
3Targeting protein for Xklp2COMPLEX#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDOrgan
12sus scrofa (pig)9823brain
23Homo sapiens (human)9606
Source (recombinant)Organism: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
Strain: sf21
Buffer solutionpH: 6.8 / Details: BRB80
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 288 K / Details: blot for 4 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 27.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 2000

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Processing

SoftwareName: REFMAC / Version: 5.8.0091 / Classification: refinement
EM software
IDNameCategory
1Appionparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9EMANinitial Euler assignment
10FREALIGNfinal Euler assignment
12FREALIGN3D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -25.74 ° / Axial rise/subunit: 9.03 Å / Axial symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85000 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL
RefinementResolution: 3.3→212.8 Å / Cor.coef. Fo:Fc: 0.739 / SU B: 32.923 / SU ML: 0.53 / ESU R: 1.625
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.3969 --
obs0.3969 191280 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 31.217 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å2-0.2 Å20.01 Å2
2--7.03 Å2-0.47 Å2
3----3.19 Å2
Refinement stepCycle: 1 / Total: 41136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01942070
ELECTRON MICROSCOPYr_bond_other_d0.0020.0238788
ELECTRON MICROSCOPYr_angle_refined_deg1.4511.95957162
ELECTRON MICROSCOPYr_angle_other_deg0.967389218
ELECTRON MICROSCOPYr_dihedral_angle_1_deg11.6564.8475882
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.09724.1981977
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.128156769
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.07915254
ELECTRON MICROSCOPYr_chiral_restr0.0820.26252
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02148014
ELECTRON MICROSCOPYr_gen_planes_other0.0020.029904
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.8573.11120794
ELECTRON MICROSCOPYr_mcbond_other0.8573.11120793
ELECTRON MICROSCOPYr_mcangle_it1.5894.66325954
ELECTRON MICROSCOPYr_mcangle_other1.5894.66325955
ELECTRON MICROSCOPYr_scbond_it0.683.221276
ELECTRON MICROSCOPYr_scbond_other0.683.221277
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.3134.74231208
ELECTRON MICROSCOPYr_long_range_B_refined3.78527.26996104
ELECTRON MICROSCOPYr_long_range_B_other3.78527.2796105
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A52676
12C52676
21A52676
22E52676
31A52676
32J52676
41A52674
42L52674
51A52676
52K52676
61B52670
62D52670
71B52670
72F52670
81B52668
82H52668
91B52670
92G52670
101B52668
102I52668
111C52674
112E52674
121C52674
122J52674
131C52674
132L52674
141C52674
142K52674
151D52670
152F52670
161D52668
162H52668
171D52672
172G52672
181D52670
182I52670
191T2566
192P2566
201E52672
202J52672
211E52672
212L52672
221E52672
222K52672
231F52666
232H52666
241F52670
242G52670
251F52668
252I52668
261J52674
262L52674
271J52676
272K52676
281H52674
282G52674
291H52672
292I52672
301L52674
302K52674
311G52674
312I52674
LS refinement shellResolution: 3.386→3.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.635 14319 -
Rfree-0 -
obs--100 %

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