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- PDB-9smx: CM1-activated gTuRC in complex with nascent alpha-E254D mutant mi... -

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Basic information

Entry
Database: PDB / ID: 9smx
TitleCM1-activated gTuRC in complex with nascent alpha-E254D mutant microtubules
Components
  • (Gamma-tubulin complex component ...) x 5
  • (Mitotic-spindle organizing protein ...) x 2
  • Actin, cytoplasmic 2, N-terminally processed
  • Isoform 1 of Tubulin alpha-1B chain
  • Tubulin beta-3 chain
  • Tubulin gamma-1 chain
  • Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1
KeywordsSTRUCTURAL PROTEIN / Microtubule / cytoskeleton / g-tubulin ring complex / tubulin / CDK5RAP2 / CM1 / nucleation
Function / homology
Function and homology information


basal body patch / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / tight junction assembly / mitotic spindle astral microtubule end / microtubule nucleation by interphase microtubule organizing center / netrin receptor binding / gamma-tubulin complex localization / microtubule nucleator activity ...basal body patch / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / tight junction assembly / mitotic spindle astral microtubule end / microtubule nucleation by interphase microtubule organizing center / netrin receptor binding / gamma-tubulin complex localization / microtubule nucleator activity / negative regulation of centriole replication / regulation of mitotic cell cycle spindle assembly checkpoint / protein localization to microtubule / dorsal root ganglion development / Post-chaperonin tubulin folding pathway / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Cilium Assembly / microtubule organizing center organization / cytoskeleton-dependent intracellular transport / SUMO is proteolytically processed / polar microtubule / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / SUMOylation of transcription factors / interphase microtubule organizing center / gamma-tubulin complex / profilin binding / gamma-tubulin ring complex / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / cell projection membrane / microtubule plus-end / septin ring / SUMOylation of DNA damage response and repair proteins / mitotic spindle microtubule / protein localization to bicellular tight junction / meiotic spindle organization / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / regulation of transepithelial transport / attachment of mitotic spindle microtubules to kinetochore / morphogenesis of a polarized epithelium / microtubule nucleation / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of tubulin folding intermediates by CCT/TriC / Formation of the dystrophin-glycoprotein complex (DGC) / Gap junction degradation / Cell-extracellular matrix interactions / SUMOylation of SUMOylation proteins / dense body / microtubule plus-end binding / Gap junction assembly / microtubule bundle formation / regulation of stress fiber assembly / non-motile cilium assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / gamma-tubulin binding / Regulation of CDH1 Function / Kinesins / non-motile cilium / protein localization to centrosome / SUMOylation of RNA binding proteins / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / Assembly and cell surface presentation of NMDA receptors / COPI-independent Golgi-to-ER retrograde traffic / Sensory processing of sound by outer hair cells of the cochlea / SUMOylation of chromatin organization proteins / regulation of neuron differentiation / centrosome cycle / regulation of focal adhesion assembly / Sensory processing of sound by inner hair cells of the cochlea / Interaction between L1 and Ankyrins / COPI-dependent Golgi-to-ER retrograde traffic / sarcomere organization / apical junction complex / negative regulation of neuron differentiation / positive regulation of wound healing / mitotic spindle pole / spindle midzone / establishment of mitotic spindle orientation / negative regulation of microtubule polymerization / maintenance of blood-brain barrier / filamentous actin / pericentriolar material / NuA4 histone acetyltransferase complex / centriole replication / ciliary transition zone / cell leading edge / Recycling pathway of L1 / microtubule polymerization / myofibril / microtubule organizing center / mitotic sister chromatid segregation / ubiquitin-like protein ligase binding
Similarity search - Function
CDK5 regulatory subunit-associated protein 2 / : / CDK5 regulatory subunit-associated protein 2-like, coiled coil / MOZART2 family / Mitotic-spindle organizing gamma-tubulin ring associated / Centrosomin, N-terminal motif 1 / Centrosomin N-terminal motif 1 / Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / EB1, C-terminal ...CDK5 regulatory subunit-associated protein 2 / : / CDK5 regulatory subunit-associated protein 2-like, coiled coil / MOZART2 family / Mitotic-spindle organizing gamma-tubulin ring associated / Centrosomin, N-terminal motif 1 / Centrosomin N-terminal motif 1 / Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / : / EB1-like C-terminal motif / 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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Actins signature 1. / Beta tubulin / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Actin / Actin family / Actin / 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 / ATPase, nucleotide binding domain / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Tubulin gamma-1 chain / Actin, cytoplasmic 2 / Tubulin alpha-1B chain / Mitotic-spindle organizing protein 1 / Small ubiquitin-related modifier / Tubulin beta-3 chain / Microtubule-associated protein RP/EB family member 1 / Mitotic-spindle organizing protein 2A / Gamma-tubulin complex component 3 ...GUANOSINE-5'-TRIPHOSPHATE / Tubulin gamma-1 chain / Actin, cytoplasmic 2 / Tubulin alpha-1B chain / Mitotic-spindle organizing protein 1 / Small ubiquitin-related modifier / Tubulin beta-3 chain / Microtubule-associated protein RP/EB family member 1 / Mitotic-spindle organizing protein 2A / Gamma-tubulin complex component 3 / Gamma-tubulin complex component 6 / Gamma-tubulin complex component 5 / CDK5 regulatory subunit-associated protein 2 / Gamma-tubulin complex component 2 / Gamma-tubulin complex component 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsLlorca, O. / Serna, M. / Lopez-Perrote, A.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)MCIN/AEI/10.13039/501100011033 Spain
European Regional Development FundPID2023-146110NB-I00European Union
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of human γTuRC closure during CM1-activated microtubule nucleation.
Authors: Marina Serna / Cláudia Brito / Silvia Speroni / Fabian Zimmermann / Andrés Lopez-Perrote / Maria Gili / Cristina Lacasa / Jens Lüders / Thomas Surrey / Oscar Llorca /
Abstract: Microtubule nucleation by the γ-tubulin ring complex (γTuRC) is spatiotemporally regulated and in higher eukaryotes is thought to involve a transition from an inactive open to an active closed ...Microtubule nucleation by the γ-tubulin ring complex (γTuRC) is spatiotemporally regulated and in higher eukaryotes is thought to involve a transition from an inactive open to an active closed conformation that matches the microtubule geometry. However, γTuRC activators only promote a partially closed conformation, raising the question of whether complete closure is required for activation. Combining in vitro nucleation assays and cryo-EM, we find that centrosomin motif 1 (CM1), a conserved element of several γTuRC regulators, potently accelerates human γTuRC-mediated microtubule nucleation by facilitating complete closure of γTuRC as the nascent microtubule assembles. A 3.7 Å cryo-EM structure identifies the γTuRC latch and several interactions involved in conformational closure. Notably, the distinct subunits that keep γTuRC open and inactive in higher eukaryotes also participate in its closure and activation. This work provides additional insight into the logic of the human γTuRC architecture and its activation by CM1.
History
DepositionSep 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
3: Gamma-tubulin complex component 3
4: Mitotic-spindle organizing protein 1
5: Gamma-tubulin complex component 6
6: Mitotic-spindle organizing protein 1
7: Actin, cytoplasmic 2, N-terminally processed
A: Gamma-tubulin complex component 2
AC: Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1
B: Gamma-tubulin complex component 3
BA: Isoform 1 of Tubulin alpha-1B chain
BB: Tubulin beta-3 chain
C: Gamma-tubulin complex component 2
CA: Isoform 1 of Tubulin alpha-1B chain
CB: Tubulin beta-3 chain
CC: Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1
CM: Mitotic-spindle organizing protein 2A
CN: Gamma-tubulin complex component 2
Cc: Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1
D: Gamma-tubulin complex component 3
DA: Isoform 1 of Tubulin alpha-1B chain
DB: Tubulin beta-3 chain
E: Gamma-tubulin complex component 2
EA: Isoform 1 of Tubulin alpha-1B chain
EB: Tubulin beta-3 chain
EC: Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1
EM: Mitotic-spindle organizing protein 2A
EN: Gamma-tubulin complex component 2
Ec: Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1
F: Gamma-tubulin complex component 3
FA: Isoform 1 of Tubulin alpha-1B chain
FB: Tubulin beta-3 chain
G: Gamma-tubulin complex component 2
GA: Isoform 1 of Tubulin alpha-1B chain
GB: Tubulin beta-3 chain
GC: Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1
GM: Mitotic-spindle organizing protein 2A
GN: Gamma-tubulin complex component 2
Gc: Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1
H: Gamma-tubulin complex component 3
HA: Isoform 1 of Tubulin alpha-1B chain
HB: Tubulin beta-3 chain
I: Gamma-tubulin complex component 4
IA: Isoform 1 of Tubulin alpha-1B chain
IB: Tubulin beta-3 chain
J: Gamma-tubulin complex component 5
JA: Isoform 1 of Tubulin alpha-1B chain
JB: Tubulin beta-3 chain
K: Gamma-tubulin complex component 4
KA: Isoform 1 of Tubulin alpha-1B chain
KB: Tubulin beta-3 chain
L: Gamma-tubulin complex component 6
LA: Isoform 1 of Tubulin alpha-1B chain
LB: Tubulin beta-3 chain
M: Gamma-tubulin complex component 2
MC: Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1
MM: Mitotic-spindle organizing protein 2A
Mc: Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1
N: Gamma-tubulin complex component 3
Y: Mitotic-spindle organizing protein 1
Z: Gamma-tubulin complex component 5
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
k: Tubulin gamma-1 chain
l: Tubulin gamma-1 chain
m: Tubulin gamma-1 chain
n: Tubulin gamma-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,442,40784
Polymers4,436,65273
Non-polymers5,75511
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Gamma-tubulin complex component ... , 5 types, 20 molecules 3BDFHN5LACCNEENGGNMIKJZ

#1: 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.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96CW5
#3: Protein Gamma-tubulin complex component 6 / GCP-6


Mass: 200733.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96RT7
#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.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BSJ2
#10: 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
#11: Protein Gamma-tubulin complex component 5 / GCP-5


Mass: 118467.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96RT8

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Mitotic-spindle organizing protein ... , 2 types, 7 molecules 46YCMEMGMMM

#2: Protein Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing protein associated with a ring of gamma-tubulin 1


Mass: 8485.724 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q08AG7
#9: Protein
Mitotic-spindle organizing protein 2A / Mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A


Mass: 16240.576 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P582

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Protein , 5 types, 46 molecules 7ACCCCcECEcGCGcMCMcBACADAEAFAGAHAIAJAKALABBCBDBEBFBGBHBIBJB...

#4: Protein Actin, cytoplasmic 2, N-terminally processed


Mass: 41723.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63261
#6: Protein
Ubiquitin-like protein SMT3,CDK5 regulatory subunit-associated protein 2,Microtubule-associated protein RP/EB family member 1 / CDK5 activator-binding protein C48 / Centrosome-associated protein 215 / APC-binding protein EB1 / ...CDK5 activator-binding protein C48 / Centrosome-associated protein 215 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 26765.963 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) Homo sapiens (human)
Gene: SMT3, YDR510W, D9719.15, CDK5RAP2, CEP215, KIAA1633, MAPRE1
Production host: Escherichia coli (E. coli)
References: UniProt: Q12306, UniProt: Q96SN8, UniProt: Q15691
#7: Protein
Isoform 1 of Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50190.418 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBA1B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P68363, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#8: Protein
Tubulin beta-3 chain / Tubulin beta-4 chain / Tubulin beta-III


Mass: 50906.703 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBB3, TUBB4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13509
#12: 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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Non-polymers , 1 types, 11 molecules

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


Mass: 523.180 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationN

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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: #1-#12 / 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 R1.2/1.3
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 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: 40.01 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 23663

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2REFMAC5.8.0267model refinement
3EPUimage acquisition
5CTFFIND4CTF correction
10cryoSPARC4.7.0initial Euler assignment
11RELION5initial Euler assignment
12RELION5final Euler assignment
14RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1776484
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 652699 / 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

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