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- PDB-5n5n: Cryo-EM structure of tsA201 cell alpha1B and betaI and betaIVb mi... -

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Basic information

Entry
Database: PDB / ID: 5n5n
TitleCryo-EM structure of tsA201 cell alpha1B and betaI and betaIVb microtubules
Components
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / Microtubules Dynamics Tubulin Isoform
Function / homology
Function and homology information


odontoblast differentiation / Cilium Assembly / Post-chaperonin tubulin folding pathway / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly ...odontoblast differentiation / Cilium Assembly / Post-chaperonin tubulin folding pathway / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / Kinesins / Assembly and cell surface presentation of NMDA receptors / COPI-independent Golgi-to-ER retrograde traffic / GTPase activating protein binding / natural killer cell mediated cytotoxicity / COPI-dependent Golgi-to-ER retrograde traffic / nuclear envelope lumen / regulation of synapse organization / Recycling pathway of L1 / RHOH GTPase cycle / MHC class I protein binding / microtubule-based process / RHO GTPases activate IQGAPs / Hedgehog 'off' state / intercellular bridge / COPI-mediated anterograde transport / cytoplasmic microtubule / Activation of AMPK downstream of NMDARs / cellular response to interleukin-4 / ciliary tip / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / Translocation of SLC2A4 (GLUT4) to the plasma membrane / sperm end piece / sperm principal piece / RHO GTPases Activate Formins / PKR-mediated signaling / microtubule cytoskeleton organization / structural constituent of cytoskeleton / HCMV Early Events / cytoplasmic ribonucleoprotein granule / Aggrephagy / mitotic spindle / azurophil granule lumen / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / cell body / Potential therapeutics for SARS / microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoskeleton / cilium / membrane raft / protein domain specific binding / cell division / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / GTP binding / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsVemu, A. / Atherton, J. / Spector, J.O. / Moores, C.A. / Roll-Mecak, A.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
Intramural Programs of the NINDS and the NHLBI, National Institutes of Health United States
CitationJournal: Mol Biol Cell / Year: 2017
Title: Tubulin isoform composition tunes microtubule dynamics.
Authors: Annapurna Vemu / Joseph Atherton / Jeffrey O Spector / Carolyn A Moores / Antonina Roll-Mecak /
Abstract: Microtubules polymerize and depolymerize stochastically, a behavior essential for cell division, motility, and differentiation. While many studies advanced our understanding of how microtubule- ...Microtubules polymerize and depolymerize stochastically, a behavior essential for cell division, motility, and differentiation. While many studies advanced our understanding of how microtubule-associated proteins tune microtubule dynamics in trans, we have yet to understand how tubulin genetic diversity regulates microtubule functions. The majority of in vitro dynamics studies are performed with tubulin purified from brain tissue. This preparation is not representative of tubulin found in many cell types. Here we report the 4.2-Å cryo-electron microscopy (cryo-EM) structure and in vitro dynamics parameters of α1B/βI+βIVb microtubules assembled from tubulin purified from a human embryonic kidney cell line with isoform composition characteristic of fibroblasts and many immortalized cell lines. We find that these microtubules grow faster and transition to depolymerization less frequently compared with brain microtubules. Cryo-EM reveals that the dynamic ends of α1B/βI+βIVb microtubules are less tapered and that these tubulin heterodimers display lower curvatures. Interestingly, analysis of EB1 distributions at dynamic ends suggests no differences in GTP cap sizes. Last, we show that the addition of recombinant α1A/βIII tubulin, a neuronal isotype overexpressed in many tumors, proportionally tunes the dynamics of α1B/βI+βIVb microtubules. Our study is an important step toward understanding how tubulin isoform composition tunes microtubule dynamics.
History
DepositionFeb 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
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
Revision 1.4May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low / _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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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
B: Tubulin beta chain
K: Tubulin alpha-1B chain
G: Tubulin alpha-1B chain
H: Tubulin alpha-1B chain
I: Tubulin alpha-1B chain
J: Tubulin alpha-1B chain
L: Tubulin alpha-1B chain
A: Tubulin beta chain
C: Tubulin beta chain
D: Tubulin beta chain
E: Tubulin beta chain
F: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)584,96336
Polymers578,40512
Non-polymers6,55824
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54520 Å2
ΔGint-306 kcal/mol
Surface area176740 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11B
21A
12B
22C
13B
23D
14B
24E
15B
25F
16K
26G
17K
27H
18K
28I
19K
29J
110K
210L
111G
211H
112G
212I
113G
213J
114G
214L
115H
215I
116H
216J
117H
217L
118I
218J
119I
219L
120J
220L
121A
221C
122A
222D
123A
223E
124A
224F
125C
225D
126C
226E
127C
227F
128D
228E
129D
229F
130E
230F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNBA1 - 4361 - 426
21GLNGLNAH1 - 4361 - 426
12GLNGLNBA1 - 4361 - 426
22GLNGLNCI1 - 4361 - 426
13GLNGLNBA1 - 4361 - 426
23GLNGLNDJ1 - 4361 - 426
14GLNGLNBA1 - 4361 - 426
24GLNGLNEK1 - 4361 - 426
15GLNGLNBA1 - 4361 - 426
25GLNGLNFL1 - 4361 - 426
16VALVALKB1 - 4371 - 437
26VALVALGC1 - 4371 - 437
17VALVALKB1 - 4371 - 437
27VALVALHD1 - 4371 - 437
18VALVALKB1 - 4371 - 437
28VALVALIE1 - 4371 - 437
19VALVALKB1 - 4371 - 437
29VALVALJF1 - 4371 - 437
110VALVALKB1 - 4371 - 437
210VALVALLG1 - 4371 - 437
111VALVALGC1 - 4371 - 437
211VALVALHD1 - 4371 - 437
112VALVALGC1 - 4371 - 437
212VALVALIE1 - 4371 - 437
113VALVALGC1 - 4371 - 437
213VALVALJF1 - 4371 - 437
114VALVALGC1 - 4371 - 437
214VALVALLG1 - 4371 - 437
115VALVALHD1 - 4371 - 437
215VALVALIE1 - 4371 - 437
116VALVALHD1 - 4371 - 437
216VALVALJF1 - 4371 - 437
117VALVALHD1 - 4371 - 437
217VALVALLG1 - 4371 - 437
118VALVALIE1 - 4371 - 437
218VALVALJF1 - 4371 - 437
119VALVALIE1 - 4371 - 437
219VALVALLG1 - 4371 - 437
120VALVALJF1 - 4371 - 437
220VALVALLG1 - 4371 - 437
121GLNGLNAH1 - 4361 - 426
221GLNGLNCI1 - 4361 - 426
122GLNGLNAH1 - 4361 - 426
222GLNGLNDJ1 - 4361 - 426
123GLNGLNAH1 - 4361 - 426
223GLNGLNEK1 - 4361 - 426
124GLNGLNAH1 - 4361 - 426
224GLNGLNFL1 - 4361 - 426
125GLNGLNCI1 - 4361 - 426
225GLNGLNDJ1 - 4361 - 426
126GLNGLNCI1 - 4361 - 426
226GLNGLNEK1 - 4361 - 426
127GLNGLNCI1 - 4361 - 426
227GLNGLNFL1 - 4361 - 426
128GLNGLNDJ1 - 4361 - 426
228GLNGLNEK1 - 4361 - 426
129GLNGLNDJ1 - 4361 - 426
229GLNGLNFL1 - 4361 - 426
130GLNGLNEK1 - 4361 - 426
230GLNGLNFL1 - 4361 - 426

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

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Components

#1: Protein
Tubulin beta chain / Tubulin beta-5 chain


Mass: 47735.793 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: GMPCPP (GTP-analogue) bound / Source: (gene. exp.) Homo sapiens (human) / Cell line: tsA201 cells / Gene: TUBB, TUBB5, OK/SW-cl.56 / Cell line (production host): tsA201 cells / Production host: Homo sapiens (human) / References: UniProt: P07437
#2: Protein
Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 48665.027 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: GTP-bound / Source: (gene. exp.) Homo sapiens (human) / Cell line: tsA201 cells / Gene: TUBA1B / Cell line (production host): tsA201 cells / Production host: Homo sapiens (human) / References: UniProt: P68363
#3: 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
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: 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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human tsA201 cell tubulin microtubules / Type: COMPLEX
Details: Microtubules formed from tsA201 cell tubulin (14pf) with bound GTP analogue GMPCPP. Tubulin was purified via TOG affinity.
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6.8
Details: BRB80 with GMPCPP (80mM PIPES, 2mM MgCl2, 1mM EGTA, 1mM DTT, 1mM GMPCPP)
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Microtubules polymerised at 25mg/ml in BRB80 with GMPCPP and diluted to a final concentration of 2.5mg/ml
Specimen supportGrid material: COPPER / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)
Image scansSampling size: 1.221 µm

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Processing

SoftwareName: REFMAC / Version: 5.8.0135 / Classification: refinement
EM software
IDNameCategory
1EMANparticle selection
2SerialEMimage acquisition
7UCSF Chimeramodel fitting
10FREALIGNfinal Euler assignment
12FREALIGN3D reconstruction
13Cootmodel refinement
14PHENIXmodel refinement
15REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13000
Details: Gold-standard high-resolution noise substitution test employed in resolution estimation (Chen et al., 2013)
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
RefinementResolution: 4.2→4.2 Å / Cor.coef. Fo:Fc: 0.812 / SU B: 81.863 / SU ML: 0.956
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.44092 --
obs0.44092 102758 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.218 Å2
Baniso -1Baniso -2Baniso -3
1--5.48 Å21.19 Å2-0.85 Å2
2--1.44 Å21.47 Å2
3---4.04 Å2
Refinement stepCycle: 1 / Total: 40470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01941382
ELECTRON MICROSCOPYr_bond_other_d0.0010.0238220
ELECTRON MICROSCOPYr_angle_refined_deg1.1351.95956220
ELECTRON MICROSCOPYr_angle_other_deg0.867387870
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.94255094
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.96624.1231950
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.097156684
ELECTRON MICROSCOPYr_dihedral_angle_4_deg9.64215252
ELECTRON MICROSCOPYr_chiral_restr0.0650.26174
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.02147094
ELECTRON MICROSCOPYr_gen_planes_other0.0010.029738
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_it0.7116.70220466
ELECTRON MICROSCOPYr_mcbond_other0.7116.70220465
ELECTRON MICROSCOPYr_mcangle_it1.34910.05225530
ELECTRON MICROSCOPYr_mcangle_other1.34910.05225531
ELECTRON MICROSCOPYr_scbond_it0.3276.73120916
ELECTRON MICROSCOPYr_scbond_other0.3276.73120909
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other0.71710.05630681
ELECTRON MICROSCOPYr_long_range_B_refined2.97956.28657454
ELECTRON MICROSCOPYr_long_range_B_other2.97856.28757451
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
11B49120
12A49120
21B49118
22C49118
31B49116
32D49116
41B49120
42E49120
51B49120
52F49120
61K49634
62G49634
71K49634
72H49634
81K49634
82I49634
91K49634
92J49634
101K49634
102L49634
111G49636
112H49636
121G49634
122I49634
131G49634
132J49634
141G49634
142L49634
151H49634
152I49634
161H49634
162J49634
171H49634
172L49634
181I49634
182J49634
191I49634
192L49634
201J49634
202L49634
211A49122
212C49122
221A49118
222D49118
231A49120
232E49120
241A49124
242F49124
251C49118
252D49118
261C49118
262E49118
271C49122
272F49122
281D49116
282E49116
291D49118
292F49118
301E49120
302F49120
LS refinement shellResolution: 4→4.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.548 7593 -
obs--100 %

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