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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 / netrin receptor binding / microtubule nucleation by interphase microtubule organizing center / 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 / netrin receptor binding / microtubule nucleation by interphase microtubule organizing center / 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) / SUMO is proteolytically processed / Cilium Assembly / microtubule organizing center organization / cytoskeleton-dependent intracellular transport / polar microtubule / Carboxyterminal post-translational modifications of tubulin / SUMOylation of transcription factors / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / interphase microtubule organizing center / gamma-tubulin complex / Postmitotic nuclear pore complex (NPC) reformation / gamma-tubulin ring complex / profilin binding / SUMOylation of transcription cofactors / septin ring / cell projection membrane / microtubule plus-end / 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 / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / microtubule nucleation / Formation of tubulin folding intermediates by CCT/TriC / 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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / non-motile cilium assembly / gamma-tubulin binding / Regulation of CDH1 Function / Kinesins / non-motile cilium / Prefoldin mediated transfer of substrate to CCT/TriC / SUMOylation of RNA binding proteins / protein localization to centrosome / 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 / Interaction between L1 and Ankyrins / regulation of focal adhesion assembly / Sensory processing of sound by inner hair cells of the cochlea / 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 / negative regulation of microtubule polymerization / establishment of mitotic spindle orientation / maintenance of blood-brain barrier / pericentriolar material / NuA4 histone acetyltransferase complex / filamentous actin / ciliary transition zone / centriole replication / cell leading edge / Recycling pathway of L1 / microtubule polymerization / myofibril / mitotic sister chromatid segregation / microtubule organizing center / 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 gamma TuRC closure during CM1-activated microtubule nucleation.
Authors: Serna, M. / Brito, C. / Speroni, S. / Zimmermann, F. / Lopez-Perrote, A. / Gili, M. / Lacasa, C. / Luders, J. / Surrey, T. / Llorca, O.
History
DepositionSep 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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