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- PDB-9g3z: Structure of the Open gamma-Tubulin Ring Complex from Pig Brain -

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Basic information

Entry
Database: PDB / ID: 9g3z
TitleStructure of the Open gamma-Tubulin Ring Complex from Pig Brain
Components
  • (Gamma-tubulin complex ...) x 4
  • (Tubulin gamma ...) x 2
  • CDK5 regulatory subunit-associated protein 2
  • Mitotic spindle organizing protein 1
  • Mitotic-spindle organizing protein 2A isoform X4
KeywordsSTRUCTURAL PROTEIN / Tubulin Complex
Function / homology
Function and homology information


gamma-tubulin complex localization / Recruitment of mitotic centrosome proteins and complexes / microtubule nucleator activity / polar microtubule / gamma-tubulin complex / gamma-tubulin ring complex / meiotic spindle organization / microtubule nucleation / gamma-tubulin binding / Recruitment of NuMA to mitotic centrosomes ...gamma-tubulin complex localization / Recruitment of mitotic centrosome proteins and complexes / microtubule nucleator activity / polar microtubule / gamma-tubulin complex / gamma-tubulin ring complex / meiotic spindle organization / microtubule nucleation / gamma-tubulin binding / Recruitment of NuMA to mitotic centrosomes / pericentriolar material / mitotic sister chromatid segregation / spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / centriole / mitotic spindle organization / meiotic cell cycle / spindle microtubule / brain development / microtubule cytoskeleton organization / spindle / neuron migration / spindle pole / cell junction / mitotic cell cycle / microtubule binding / microtubule / calmodulin binding / ciliary basal body / centrosome / GTP binding / Golgi apparatus / nucleoplasm / nucleus / cytoplasm
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 / Gamma-tubulin complex component 6, N-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 / 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
CDK5 regulatory subunit-associated protein 2 / Gamma-tubulin complex component / Tubulin gamma chain / Mitotic spindle organizing protein 1 / Gamma-tubulin complex component / Gamma-tubulin complex component / Gamma-tubulin complex component 6 / Mitotic-spindle organizing protein 2A isoform X4 / Gamma-tubulin complex component 3
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMunoz-Hernandez, H. / Wieczorek, M.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationTMSGI3_211309 Switzerland
Swiss National Science Foundation310030_208120 Switzerland
CitationJournal: Dev Cell / Year: 2024
Title: Partial closure of the γ-tubulin ring complex by CDK5RAP2 activates microtubule nucleation.
Authors: Yixin Xu / Hugo Muñoz-Hernández / Rościsław Krutyhołowa / Florina Marxer / Ferdane Cetin / Michal Wieczorek /
Abstract: Microtubule nucleation is templated by the γ-tubulin ring complex (γ-TuRC), but its structure deviates from the geometry of α-/β-tubulin in the microtubule, explaining the complex's poor ...Microtubule nucleation is templated by the γ-tubulin ring complex (γ-TuRC), but its structure deviates from the geometry of α-/β-tubulin in the microtubule, explaining the complex's poor nucleating activity. Several proteins may activate the γ-TuRC, but the mechanisms underlying activation are not known. Here, we determined the structure of the porcine γ-TuRC purified using CDK5RAP2's centrosomin motif 1 (CM1). We identified an unexpected conformation of the γ-TuRC bound to multiple protein modules containing MZT2, GCP2, and CDK5RAP2, resulting in a long-range constriction of the γ-tubulin ring that brings it in closer agreement with the 13-protofilament microtubule. Additional CDK5RAP2 promoted γ-TuRC decoration and stimulated the microtubule-nucleating activities of the porcine γ-TuRC and a reconstituted, CM1-free human complex in single-molecule assays. Our results provide a structural mechanism for the control of microtubule nucleation by CM1 proteins and identify conformational transitions in the γ-TuRC that prime it for microtubule nucleation.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Dec 18, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Mitotic spindle organizing protein 1
P: Mitotic spindle organizing protein 1
Q: Mitotic spindle organizing protein 1
Y: Mitotic-spindle organizing protein 2A isoform X4
a: Tubulin gamma chain
m: Tubulin gamma chain
w: CDK5 regulatory subunit-associated protein 2
x: CDK5 regulatory subunit-associated protein 2
N: Gamma-tubulin complex component 3
M: Gamma-tubulin complex component
L: Tubulin gamma complex associated protein 6
A: Gamma-tubulin complex component
B: Gamma-tubulin complex component 3
C: Gamma-tubulin complex component
H: Gamma-tubulin complex component 3
D: Gamma-tubulin complex component 3
E: Gamma-tubulin complex component
F: Gamma-tubulin complex component 3
G: Gamma-tubulin complex component
I: Gamma-tubulin complex component
b: Tubulin gamma chain
c: Tubulin gamma chain
d: Tubulin gamma chain
e: Tubulin gamma chain
f: Tubulin gamma chain
g: Tubulin gamma chain
h: Tubulin gamma chain
i: Tubulin gamma chain
n: Tubulin gamma chain
K: Gamma-tubulin complex component
J: Gamma-tubulin complex component
k: Tubulin gamma chain
j: Tubulin gamma chain
l: Tubulin gamma chain


Theoretical massNumber of molelcules
Total (without water)2,626,34234
Polymers2,626,34234
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 6 molecules OPQYwx

#1: Protein Mitotic spindle organizing protein 1


Mass: 8285.489 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MZT1 / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1VBW8
#2: Protein Mitotic-spindle organizing protein 2A isoform X4


Mass: 15920.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: LOC100153925 / Production host: Sus scrofa (pig) / References: UniProt: F1RK97
#4: Protein CDK5 regulatory subunit-associated protein 2


Mass: 189905.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Human sequence used for CDK5RAP251-100 / Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5RAP2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0MRG9

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Tubulin gamma ... , 2 types, 15 molecules ambcdefghinkjlL

#3: Protein
Tubulin gamma chain


Mass: 51135.562 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBG2 / Production host: Sus scrofa (pig) / References: UniProt: A0A287BRH5
#7: Protein Tubulin gamma complex associated protein 6


Mass: 188644.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBGCP6 / Production host: Sus scrofa (pig) / References: UniProt: A0A8W4FDV6

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Gamma-tubulin complex ... , 4 types, 13 molecules NBHDFMACEGIKJ

#5: Protein
Gamma-tubulin complex component 3 / Tubulin gamma complex associated protein 3


Mass: 103172.477 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBGCP3 / Production host: Sus scrofa (pig) / References: UniProt: F1RN46
#6: Protein
Gamma-tubulin complex component


Mass: 102609.703 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: UniProt: A0A8D1IGH3
#8: Protein Gamma-tubulin complex component


Mass: 76104.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBGCP4 / Production host: Sus scrofa (pig) / References: UniProt: A0A8D1V2H0
#9: Protein Gamma-tubulin complex component


Mass: 120090.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: UniProt: A0A287B1K1

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Details

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 from native pig brain / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE-PROPANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80608 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 247.43 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002478226
ELECTRON MICROSCOPYf_angle_d0.5901108889
ELECTRON MICROSCOPYf_chiral_restr0.039115056
ELECTRON MICROSCOPYf_plane_restr0.004215713
ELECTRON MICROSCOPYf_dihedral_angle_d5.273115713

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