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- PDB-8q62: Early closed conformation of the g-tubulin ring complex -

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Basic information

Entry
Database: PDB / ID: 8q62
TitleEarly closed conformation of the g-tubulin ring complex
Components
  • (Gamma-tubulin complex component ...) x 5
  • Tubulin gamma-1 chain
KeywordsSTRUCTURAL PROTEIN / Microtubule / cytoskeleton / g-tubulin ring complex / tubulin
Function / homology
Function and homology information


microtubule nucleator activity / polar microtubule / gamma-tubulin complex / gamma-tubulin ring complex / mitotic spindle microtubule / meiotic spindle organization / microtubule nucleation / gamma-tubulin binding / non-motile cilium / pericentriolar material ...microtubule nucleator activity / polar microtubule / gamma-tubulin complex / gamma-tubulin ring complex / mitotic spindle microtubule / meiotic spindle organization / microtubule nucleation / gamma-tubulin binding / non-motile cilium / pericentriolar material / cell leading edge / microtubule organizing center / mitotic sister chromatid segregation / single fertilization / spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / centriole / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / condensed nuclear chromosome / mitotic spindle organization / meiotic cell cycle / brain development / recycling endosome / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / neuron migration / apical part of cell / spindle pole / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / microtubule cytoskeleton / protein-containing complex assembly / microtubule binding / microtubule / neuron projection / cilium / ciliary basal body / centrosome / GTP binding / structural molecule activity / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Gamma-tubulin complex component 6, N-terminal / Gamma-tubulin complex component 6 N-terminus / Gamma tubulin / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal / Tubulin ...Gamma-tubulin complex component 6, N-terminal / Gamma-tubulin complex component 6 N-terminus / Gamma tubulin / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal / 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
Similarity search - Domain/homology
Tubulin gamma-1 chain / Gamma-tubulin complex component 3 / Gamma-tubulin complex component 6 / Gamma-tubulin complex component 5 / Gamma-tubulin complex component 2 / Gamma-tubulin complex component 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsLlorca, O. / Serna, M. / Fernandez-Leiro, R.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)AEI/10.13039/501100011 003 Spain
European Regional Development FundPID2020-114429RB-I00European Union
CitationJournal: Science / Year: 2024
Title: Transition of human γ-tubulin ring complex into a closed conformation during microtubule nucleation.
Authors: Cláudia Brito / Marina Serna / Pablo Guerra / Oscar Llorca / Thomas Surrey /
Abstract: Microtubules are essential for intracellular organization and chromosome segregation. They are nucleated by the γ-tubulin ring complex (γTuRC). However, isolated vertebrate γTuRC adopts an open ...Microtubules are essential for intracellular organization and chromosome segregation. They are nucleated by the γ-tubulin ring complex (γTuRC). However, isolated vertebrate γTuRC adopts an open conformation that deviates from the microtubule structure, raising the question of the nucleation mechanism. In this study, we determined cryo-electron microscopy structures of human γTuRC bound to a nascent microtubule. Structural changes of the complex into a closed conformation ensure that γTuRC templates the 13-protofilament microtubules that exist in human cells. Closure is mediated by a latch that interacts with incorporating tubulin, making it part of the closing mechanism. Further rearrangements involve all γTuRC subunits and the removal of the actin-containing luminal bridge. Our proposed mechanism of microtubule nucleation by human γTuRC relies on large-scale structural changes that are likely the target of regulation in cells.
History
DepositionAug 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
k: Tubulin gamma-1 chain
J: Gamma-tubulin complex component 5
K: Gamma-tubulin complex component 4
B: Gamma-tubulin complex component 3
C: Gamma-tubulin complex component 2
D: Gamma-tubulin complex component 3
E: Gamma-tubulin complex component 2
F: Gamma-tubulin complex component 3
G: Gamma-tubulin complex component 2
H: Gamma-tubulin complex component 3
I: Gamma-tubulin complex component 4
L: Gamma-tubulin complex component 6
M: Gamma-tubulin complex component 2
N: Gamma-tubulin complex component 3
A: Gamma-tubulin complex component 2
a: Tubulin gamma-1 chain
b: Tubulin gamma-1 chain
c: Tubulin gamma-1 chain
d: Tubulin gamma-1 chain
e: Tubulin gamma-1 chain
f: Tubulin gamma-1 chain
g: Tubulin gamma-1 chain
h: Tubulin gamma-1 chain
i: Tubulin gamma-1 chain
j: Tubulin gamma-1 chain
l: Tubulin gamma-1 chain
m: Tubulin gamma-1 chain
n: Tubulin gamma-1 chain


Theoretical massNumber of molelcules
Total (without water)2,220,63528
Polymers2,220,63528
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515
1616
1717
1818
1919
2020
2121
2222
2323
2424
2525
2626
2727
2828
2929
3030
3131
3232
3333
3434
3535
3636
3737
3838
3939
4040
4141
4242
4343
4444
4545
4646
4747
4848
4949
5050
5151
5252
5353
5454
5555
5656
5757
5858
5959
6060
6161
6262
6363
6464
6565
6666
6767
6868
6969
7070
7171
7272
7373
7474
7575
7676
7777
7878
7979
8080
8181
8282
8383
8484
8585
8686
8787
8888
8989
9090
9191
9292
9393
9494
9595
9696
9797
9898
9999
100100
101101
102102
103103
104104
105105
106106
107107
108108
109109
110110
111111
112112

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
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26
27
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29
30
31
32
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42
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47
48
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50
51
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53
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55
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81
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85
86
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91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112

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Components

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Protein , 1 types, 14 molecules kabcdefghijlmn

#1: Protein
Tubulin gamma-1 chain / Gamma-1-tubulin / Gamma-tubulin complex component 1 / GCP-1


Mass: 51227.770 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P23258

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Gamma-tubulin complex component ... , 5 types, 14 molecules JKIBDFHNCEGMAL

#2: Protein Gamma-tubulin complex component 5 / GCP-5


Mass: 118467.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96RT8
#3: Protein Gamma-tubulin complex component 4 / hGCP4 / Gamma-ring complex protein 76 kDa / hGrip76


Mass: 76179.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UGJ1
#4: Protein
Gamma-tubulin complex component 3 / hGCP3 / Gamma-ring complex protein 104 kDa / hGrip104 / Spindle pole body protein Spc98 homolog / hSpc98


Mass: 103710.102 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96CW5
#5: Protein
Gamma-tubulin complex component 2 / hGCP2 / Gamma-ring complex protein 103 kDa / hGrip103 / Spindle pole body protein Spc97 homolog / hSpc97


Mass: 102666.953 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BSJ2
#6: Protein Gamma-tubulin complex component 6 / GCP-6


Mass: 200733.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96RT7

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: gamma-tubulin ring complex / Type: COMPLEX / Entity ID: #2-#4, #1, #6 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 6.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 310 K

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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 / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.3 sec. / Electron dose: 46.276 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 46276

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Processing

EM softwareName: REFMAC / Version: 5.8.0267 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1580023
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 357509 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17AS4

7as4

17AS41PDBexperimental model
26X0U

6x0u

16X0U2PDBexperimental model
RefinementResolution: 3.72→3.72 Å / Cor.coef. Fo:Fc: 0.932 / SU B: 136.13 / SU ML: 1.614 / ESU R: 1.014
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.5141 --
obs0.5141 939214 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 117.195 Å2
Refinement stepCycle: 1 / Total: 115794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.013118242
ELECTRON MICROSCOPYr_bond_other_d0.0080.017112695
ELECTRON MICROSCOPYr_angle_refined_deg1.4691.638159952
ELECTRON MICROSCOPYr_angle_other_deg1.4541.577258893
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.155514140
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.05522.0196612
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.2931521004
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.75515845
ELECTRON MICROSCOPYr_chiral_restr0.0760.215250
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.02132350
ELECTRON MICROSCOPYr_gen_planes_other0.0030.0228112
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_it3.65912.47457000
ELECTRON MICROSCOPYr_mcbond_other3.65912.47456998
ELECTRON MICROSCOPYr_mcangle_it6.29518.70770992
ELECTRON MICROSCOPYr_mcangle_other6.29518.70770992
ELECTRON MICROSCOPYr_scbond_it2.85512.66161242
ELECTRON MICROSCOPYr_scbond_other2.85512.66161243
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other5.27818.92488961
ELECTRON MICROSCOPYr_long_range_B_refined13.405485933
ELECTRON MICROSCOPYr_long_range_B_other13.405485932
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11k286700.04
12a286700.04
21k286940.03
22b286940.03
31k286060.05
32c286060.05
41k287060.02
42d287060.02
51k287000.02
52e287000.02
61k286520.04
62f286520.04
71k286520.03
72g286520.03
81k287060.03
82h287060.03
91k285260.05
92i285260.05
101k286260.04
102j286260.04
111k286840.03
112l286840.03
121k285620.05
122m285620.05
131k282700.08
132n282700.08
141K250900.3
142I250900.3
151B298000.29
152D298000.29
161B302800.29
162F302800.29
171B297400.29
172H297400.29
181B297620.29
182N297620.29
191C315960.28
192E315960.28
201C318040.27
202G318040.27
211C314080.28
212M314080.28
221C302860.29
222A302860.29
231D314280.26
232F314280.26
241D302800.28
242H302800.28
251D298880.28
252N298880.28
261E344180.25
262G344180.25
271E336720.25
272M336720.25
281E312720.27
282A312720.27
291F309960.27
292H309960.27
301F308720.27
302N308720.27
311G395760.13
312M395760.13
321G307440.28
322A307440.28
331H370220.11
332N370220.11
341M305000.28
342A305000.28
351a286300.04
352b286300.04
361a286240.04
362c286240.04
371a286500.04
372d286500.04
381a286600.04
382e286600.04
391a286100.05
392f286100.05
401a286100.05
402g286100.05
411a286740.04
412h286740.04
421a284960.06
422i284960.06
431a286440.04
432j286440.04
441a286880.03
442l286880.03
451a285620.05
452m285620.05
461a282620.08
462n282620.08
471b285700.05
472c285700.05
481b286760.03
482d286760.03
491b286620.03
492e286620.03
501b286200.04
502f286200.04
511b286140.04
512g286140.04
521b286660.04
522h286660.04
531b284880.06
532i284880.06
541b286020.05
542j286020.05
551b286580.03
552l286580.03
561b285400.05
562m285400.05
571b282500.08
572n282500.08
581c286040.05
582d286040.05
591c286060.04
592e286060.04
601c285580.05
602f285580.05
611c285580.05
612g285580.05
621c286080.05
622h286080.05
631c284740.06
632i284740.06
641c285680.05
642j285680.05
651c285940.05
652l285940.05
661c284680.06
662m284680.06
671c281900.08
672n281900.08
681d287160.02
682e287160.02
691d286740.04
692f286740.04
701d286640.03
702g286640.03
711d286780.03
712h286780.03
721d285100.05
722i285100.05
731d286160.05
732j286160.05
741d286660.03
742l286660.03
751d285420.05
752m285420.05
761d282560.08
762n282560.08
771e286680.04
772f286680.04
781e287100.03
782g287100.03
791e286780.04
792h286780.04
801e284900.06
802i284900.06
811e286280.05
812j286280.05
821e286620.03
822l286620.03
831e285380.05
832m285380.05
841e282440.08
842n282440.08
851f286740.04
852g286740.04
861f286340.05
862h286340.05
871f284500.06
872i284500.06
881f286120.05
882j286120.05
891f286260.04
892l286260.04
901f284960.06
902m284960.06
911f282120.08
912n282120.08
921g286240.04
922h286240.04
931g284440.06
932i284440.06
941g286020.05
942j286020.05
951g286160.04
952l286160.04
961g284880.06
962m284880.06
971g282040.08
972n282040.08
981h285700.05
982i285700.05
991h286300.05
992j286300.05
1001h286920.03
1002l286920.03
1011h285780.05
1012m285780.05
1021h282940.08
1022n282940.08
1031i284400.06
1032j284400.06
1041i285120.05
1042l285120.05
1051i283860.07
1052m283860.07
1061i281060.09
1062n281060.09
1071j286560.04
1072l286560.04
1081j285340.06
1082m285340.06
1091j282360.08
1092n282360.08
1101l286080.05
1102m286080.05
1111l283000.08
1112n283000.08
1121m281940.09
1122n281940.09
LS refinement shellResolution: 4→4.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.567 69522 -
obs--100 %

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