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- PDB-6dpw: Undecorated GTPgammaS microtubule -

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Basic information

Entry
Database: PDB / ID: 6dpw
TitleUndecorated GTPgammaS microtubule
Components
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / microtubule / cytoskeleton / GTPgammaS / seam
Function / homology
Function and homology information


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 ...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 / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Recruitment of NuMA to mitotic centrosomes / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / COPI-mediated anterograde transport / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / microtubule / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang, R. / Nogales, E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM051487 United States
National Science Foundation (NSF, United States)1106400 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Separating the effects of nucleotide and EB binding on microtubule structure.
Authors: Rui Zhang / Benjamin LaFrance / Eva Nogales /
Abstract: Microtubules (MTs) are polymers assembled from αβ-tubulin heterodimers that display the hallmark behavior of dynamic instability. MT dynamics are driven by GTP hydrolysis within the MT lattice, and ...Microtubules (MTs) are polymers assembled from αβ-tubulin heterodimers that display the hallmark behavior of dynamic instability. MT dynamics are driven by GTP hydrolysis within the MT lattice, and are highly regulated by a number of MT-associated proteins (MAPs). How MAPs affect MTs is still not fully understood, partly due to a lack of high-resolution structural data on undecorated MTs, which need to serve as a baseline for further comparisons. Here we report three structures of MTs in different nucleotide states (GMPCPP, GDP, and GTPγS) at near-atomic resolution and in the absence of any binding proteins. These structures allowed us to differentiate the effects of nucleotide state versus MAP binding on MT structure. Kinesin binding has a small effect on the extended, GMPCPP-bound lattice, but hardly affects the compacted GDP-MT lattice, while binding of end-binding (EB) proteins can induce lattice compaction (together with lattice twist) in MTs that were initially in an extended and more stable state. We propose a MT lattice-centric model in which the MT lattice serves as a platform that integrates internal tubulin signals, such as nucleotide state, with outside signals, such as binding of MAPs or mechanical forces, resulting in global lattice rearrangements that in turn affect the affinity of other MT partners and result in the exquisite regulation of MT dynamics.
History
DepositionJun 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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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Structure viewerMolecule:
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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
E: Tubulin alpha-1B chain
F: Tubulin beta chain
G: Tubulin beta chain
H: Tubulin beta chain
I: Tubulin beta chain
J: Tubulin alpha-1B chain
K: Tubulin alpha-1B chain
L: Tubulin alpha-1B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)607,19430
Polymers600,67312
Non-polymers6,52018
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area52310 Å2
ΔGint-250 kcal/mol
Surface area167350 Å2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23J
14A
24K
15A
25L
16B
26D
17B
27F
18B
28G
19B
29H
110B
210I
111C
211E
112C
212J
113C
213K
114C
214L
115D
215F
116D
216G
117D
217H
118D
218I
119E
219J
120E
220K
121E
221L
122F
222G
123F
223H
124F
224I
125G
225H
126G
226I
127H
227I
128J
228K
129J
229L
130K
230L

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA1 - 4391 - 439
21SERSERCC1 - 4391 - 439
12SERSERAA1 - 4391 - 439
22SERSEREE1 - 4391 - 439
13SERSERAA1 - 4391 - 439
23SERSERJJ1 - 4391 - 439
14SERSERAA1 - 4391 - 439
24SERSERKK1 - 4391 - 439
15SERSERAA1 - 4391 - 439
25SERSERLL1 - 4391 - 439
16VALVALBB1 - 4291 - 419
26VALVALDD1 - 4291 - 419
17VALVALBB1 - 4291 - 419
27VALVALFF1 - 4291 - 419
18VALVALBB1 - 4291 - 419
28VALVALGG1 - 4291 - 419
19VALVALBB1 - 4291 - 419
29VALVALHH1 - 4291 - 419
110VALVALBB1 - 4291 - 419
210VALVALII1 - 4291 - 419
111SERSERCC1 - 4391 - 439
211SERSEREE1 - 4391 - 439
112SERSERCC1 - 4391 - 439
212SERSERJJ1 - 4391 - 439
113SERSERCC1 - 4391 - 439
213SERSERKK1 - 4391 - 439
114SERSERCC1 - 4391 - 439
214SERSERLL1 - 4391 - 439
115VALVALDD1 - 4291 - 419
215VALVALFF1 - 4291 - 419
116VALVALDD1 - 4291 - 419
216VALVALGG1 - 4291 - 419
117VALVALDD1 - 4291 - 419
217VALVALHH1 - 4291 - 419
118VALVALDD1 - 4291 - 419
218VALVALII1 - 4291 - 419
119SERSEREE1 - 4391 - 439
219SERSERJJ1 - 4391 - 439
120SERSEREE1 - 4391 - 439
220SERSERKK1 - 4391 - 439
121SERSEREE1 - 4391 - 439
221SERSERLL1 - 4391 - 439
122VALVALFF1 - 4291 - 419
222VALVALGG1 - 4291 - 419
123VALVALFF1 - 4291 - 419
223VALVALHH1 - 4291 - 419
124VALVALFF1 - 4291 - 419
224VALVALII1 - 4291 - 419
125VALVALGG1 - 4291 - 419
225VALVALHH1 - 4291 - 419
126VALVALGG1 - 4291 - 419
226VALVALII1 - 4291 - 419
127VALVALHH1 - 4291 - 419
227VALVALII1 - 4291 - 419
128SERSERJJ1 - 4391 - 439
228SERSERKK1 - 4391 - 439
129SERSERJJ1 - 4391 - 439
229SERSERLL1 - 4391 - 439
130SERSERKK1 - 4391 - 439
230SERSERLL1 - 4391 - 439

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 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) / 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) / References: UniProt: P02554
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3S

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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

ComponentName: GTPgammaS-microtubule polymerized from GMPCPP-microtubule seeds
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 6.8
Details: Modified BRB80 buffer (80 mM PIPES, pH 6.8, 1 mM EGTA, 0.2 mM MgCl2) supplemented with 1 mM GTPgammaS, 1 mM DTT, and 0.05% Nonident P-40
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: GTPgammaS-microtubules were polymerized at 37 degrees for 30 minutes in the presence of GMPCPP-microtubule seeds.
Specimen supportDetails: The grid was glow discharged using Solarus (Gatan Inc).
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 310 K / Details: Blot for 4 seconds before plunging.

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 27500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 1.44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 616
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 20 / Used frames/image: 1-20

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Processing

SoftwareName: REFMAC / Version: 5.8.0091 / Classification: refinement
EM software
IDNameCategory
1Appionparticle selection
2Leginonimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9EMANinitial Euler assignment
10FREALIGNfinal Euler assignment
12FREALIGN3D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -25.774 ° / Axial rise/subunit: 8.757 Å / Axial symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49145 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: HELICAL
Atomic model buildingB value: 125 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
RefinementResolution: 3.5→212.8 Å / Cor.coef. Fo:Fc: 0.824 / SU B: 43.899 / SU ML: 0.659
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.39283 --
obs0.39283 150714 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 54.777 Å2
Baniso -1Baniso -2Baniso -3
1--5.25 Å2-0.21 Å2-0.2 Å2
2--7.98 Å2-1.08 Å2
3----2.73 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01941742
ELECTRON MICROSCOPYr_bond_other_d0.0020.0238460
ELECTRON MICROSCOPYr_angle_refined_deg1.3471.95956718
ELECTRON MICROSCOPYr_angle_other_deg0.941388482
ELECTRON MICROSCOPYr_dihedral_angle_1_deg11.5374.8115839
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.67824.2071987
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.024156730
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.06215255
ELECTRON MICROSCOPYr_chiral_restr0.0760.26198
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02147658
ELECTRON MICROSCOPYr_gen_planes_other0.0020.029828
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_it2.2245.35820598
ELECTRON MICROSCOPYr_mcbond_other2.2245.35720597
ELECTRON MICROSCOPYr_mcangle_it4.0868.02625716
ELECTRON MICROSCOPYr_mcangle_other4.0868.02725717
ELECTRON MICROSCOPYr_scbond_it2.0115.65121144
ELECTRON MICROSCOPYr_scbond_other2.0115.65321132
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other3.8218.32230983
ELECTRON MICROSCOPYr_long_range_B_refined8.86346.26794746
ELECTRON MICROSCOPYr_long_range_B_other8.86446.27694724
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
11A52826
12C52826
21A52828
22E52828
31A52826
32J52826
41A52828
42K52828
51A52826
52L52826
61B52676
62D52676
71B52676
72F52676
81B52674
82G52674
91B52676
92H52676
101B52674
102I52674
111C52828
112E52828
121C52826
122J52826
131C52832
132K52832
141C52826
142L52826
151D52670
152F52670
161D52670
162G52670
171D52672
172H52672
181D52674
182I52674
191E52830
192J52830
201E52830
202K52830
211E52826
212L52826
221F52680
222G52680
231F52674
232H52674
241F52674
242I52674
251G52676
252H52676
261G52676
262I52676
271H52678
272I52678
281J52830
282K52830
291J52826
292L52826
301K52828
302L52828
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.882 11205 -
Rfree-0 -
obs--100 %

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