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- PDB-6m33: Crystal structure of Homo Sapian GCP6 N-terminus and Mozart1 -

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Basic information

Entry
Database: PDB / ID: 6m33
TitleCrystal structure of Homo Sapian GCP6 N-terminus and Mozart1
Components
  • Gamma-tubulin complex component 6
  • Mitotic-spindle organizing protein 1
KeywordsCELL CYCLE / Gamma tubulin complex / microtubule / GCP / Mzt1
Function / homology
Function and homology information


microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / equatorial microtubule organizing center / gamma-tubulin ring complex / interphase microtubule organizing center / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / mitotic spindle assembly / spindle assembly ...microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / equatorial microtubule organizing center / gamma-tubulin ring complex / interphase microtubule organizing center / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / mitotic spindle assembly / spindle assembly / cytoplasmic microtubule organization / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / meiotic cell cycle / spindle / spindle pole / mitotic cell cycle / microtubule binding / microtubule / centrosome / membrane / cytosol
Similarity search - Function
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 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
Similarity search - Domain/homology
Mitotic-spindle organizing protein 1 / Gamma-tubulin complex component 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.29434890409 Å
AuthorsHuang, T.L. / Hsia, K.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Cell Rep / Year: 2020
Title: MZT Proteins Form Multi-Faceted Structural Modules in the γ-Tubulin Ring Complex.
Authors: Michal Wieczorek / Tzu-Lun Huang / Linas Urnavicius / Kuo-Chiang Hsia / Tarun M Kapoor /
Abstract: Microtubule organization depends on the γ-tubulin ring complex (γ-TuRC), a ∼2.3-MDa nucleation factor comprising an asymmetric assembly of γ-tubulin and GCP2-GCP6. However, it is currently ...Microtubule organization depends on the γ-tubulin ring complex (γ-TuRC), a ∼2.3-MDa nucleation factor comprising an asymmetric assembly of γ-tubulin and GCP2-GCP6. However, it is currently unclear how the γ-TuRC-associated microproteins MZT1 and MZT2 contribute to the structure and regulation of the holocomplex. Here, we report cryo-EM structures of MZT1 and MZT2 in the context of the native human γ-TuRC. MZT1 forms two subcomplexes with the N-terminal α-helical domains of GCP3 or GCP6 (GCP-NHDs) within the γ-TuRC "lumenal bridge." We determine the X-ray structure of recombinant MZT1/GCP6-NHD and find it is similar to that within the native γ-TuRC. We identify two additional MZT/GCP-NHD-like subcomplexes, one of which is located on the outer face of the γ-TuRC and comprises MZT2 and GCP2-NHD in complex with a centrosomin motif 1 (CM1)-containing peptide. Our data reveal how MZT1 and MZT2 establish multi-faceted, structurally mimetic "modules" that can expand structural and regulatory interfaces in the γ-TuRC.
History
DepositionMar 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-tubulin complex component 6
B: Mitotic-spindle organizing protein 1


Theoretical massNumber of molelcules
Total (without water)22,3542
Polymers22,3542
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-43 kcal/mol
Surface area9910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.466, 69.466, 118.186
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Gamma-tubulin complex component 6 / GCP-6


Mass: 13575.808 Da / Num. of mol.: 1 / Fragment: N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBGCP6, GCP6, KIAA1669 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RT7
#2: Protein Mitotic-spindle organizing protein 1 / Mozart1 / Mitotic-spindle organizing protein associated with a ring of gamma-tubulin 1


Mass: 8778.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MZT1, C13orf37, MOZART1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08AG7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.5M Ammonium chloride, 0.1M Bis-Tris propane p.H 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 3.29→20 Å / Num. obs: 5211 / % possible obs: 98.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 149.497634035 Å2 / CC1/2: 0.997 / Net I/σ(I): 17.1
Reflection shellResolution: 3.29→3.41 Å / Num. unique obs: 505 / CC1/2: 0.695

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.29434890409→19.7705361673 Å / SU ML: 0.455939835207 / Cross valid method: FREE R-VALUE / σ(F): 1.37571273018 / Phase error: 38.6664371805
RfactorNum. reflection% reflection
Rfree0.298262414817 513 9.9844297392 %
Rwork0.222217067508 --
obs0.229930059088 5138 96.8155266629 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 165.271188327 Å2
Refinement stepCycle: LAST / Resolution: 3.29434890409→19.7705361673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 0 0 1218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01029207945511221
X-RAY DIFFRACTIONf_angle_d1.338025014811639
X-RAY DIFFRACTIONf_chiral_restr0.0622443257507208
X-RAY DIFFRACTIONf_plane_restr0.0051913972366206
X-RAY DIFFRACTIONf_dihedral_angle_d18.1185867797773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.6240.3452587774681240.2972755598321152X-RAY DIFFRACTION98.2294072363
3.624-4.14420.3604217714411270.2613606919861154X-RAY DIFFRACTION98.6143187067
4.1442-5.20550.283148579851290.2339614538381143X-RAY DIFFRACTION97.1734148205
5.2055-100.2865104846451330.1991709328171176X-RAY DIFFRACTION93.7679083095
Refinement TLS params.Method: refined / Origin x: 30.491066523 Å / Origin y: -15.8920087221 Å / Origin z: 12.2643648349 Å
111213212223313233
T1.1170432841 Å20.110434502335 Å20.170821108999 Å2-0.960953592376 Å2-0.0352820758846 Å2--0.819578883457 Å2
L7.84479815726 °23.34240594294 °21.92266603367 °2-8.08500000215 °21.09083066551 °2--8.45791574626 °2
S0.111789088331 Å °-0.29708414369 Å °-0.464639489005 Å °0.128253795392 Å °0.18992021902 Å °-0.17457073171 Å °0.779888230553 Å °0.437759739612 Å °-0.222343987678 Å °
Refinement TLS groupSelection details: all

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