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- PDB-6l81: Crystal structure of Homo sapiens GCP5 N-terminus and Mozart1 -

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Basic information

Entry
Database: PDB / ID: 6l81
TitleCrystal structure of Homo sapiens GCP5 N-terminus and Mozart1
Components
  • Gamma-tubulin complex component 5
  • Mitotic-spindle organizing protein 1
KeywordsTRANSLATION / gamma tubulin complex / microprotein / microtubule
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 / cytosol
Similarity search - Function
Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19650999049 Å
AuthorsHuang, T.L. / Wang, H.J. / Wang, S.W. / Hsia, K.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Cell Rep / Year: 2020
Title: Promiscuous Binding of Microprotein Mozart1 to gamma-Tubulin Complex Mediates Specific Subcellular Targeting to Control Microtubule Array Formation.
Authors: Huang, T.L. / Wang, H.J. / Chang, Y.C. / Wang, S.W. / Hsia, K.C.
History
DepositionNov 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: 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 5
B: Mitotic-spindle organizing protein 1
C: Gamma-tubulin complex component 5
D: Mitotic-spindle organizing protein 1


Theoretical massNumber of molelcules
Total (without water)45,8584
Polymers45,8584
Non-polymers00
Water25214
1
A: Gamma-tubulin complex component 5
B: Mitotic-spindle organizing protein 1


Theoretical massNumber of molelcules
Total (without water)22,9292
Polymers22,9292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-38 kcal/mol
Surface area9230 Å2
MethodPISA
2
C: Gamma-tubulin complex component 5
D: Mitotic-spindle organizing protein 1


Theoretical massNumber of molelcules
Total (without water)22,9292
Polymers22,9292
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-39 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.390, 96.144, 51.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 14181.072 Da / Num. of mol.: 2 / Fragment: N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBGCP5, GCP5, KIAA1899 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RT8
#2: Protein Mitotic-spindle organizing protein 1 / Mozart1 / Mitotic-spindle organizing protein associated with a ring of gamma-tubulin 1


Mass: 8748.012 Da / Num. of mol.: 2
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium iodide, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.19→28.2 Å / Num. obs: 76023 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 47.4581899538 Å2 / CC1/2: 0.997 / Net I/σ(I): 30.9
Reflection shellResolution: 2.197→2.643 Å / Num. unique obs: 13594 / CC1/2: 0.775

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.19650999049→28.1702537562 Å / SU ML: 0.295043640665 / Cross valid method: FREE R-VALUE / σ(F): 1.35991132209 / Phase error: 26.430103326
RfactorNum. reflection% reflection
Rfree0.261387014565 1990 8.72921875685 %
Rwork0.219133017853 --
obs0.222847826508 22797 98.1275826446 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.8991978804 Å2
Refinement stepCycle: LAST / Resolution: 2.19650999049→28.1702537562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 0 14 2438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007476176539172455
X-RAY DIFFRACTIONf_angle_d0.8413362283763310
X-RAY DIFFRACTIONf_chiral_restr0.0467162174148390
X-RAY DIFFRACTIONf_plane_restr0.00564493263787422
X-RAY DIFFRACTIONf_dihedral_angle_d16.16658942711497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25140.3249984049041400.2420924996081474X-RAY DIFFRACTION98.8364972443
2.2514-2.31230.3050747429161410.2356349512661487X-RAY DIFFRACTION100
2.3123-2.38030.2891163809061520.2400792861499X-RAY DIFFRACTION100
2.3803-2.45710.2855218238851300.2233571150111489X-RAY DIFFRACTION99.9382716049
2.4571-2.54480.3017010454151540.2390645577121448X-RAY DIFFRACTION99.8130841121
2.5448-2.64660.3003638742241350.2239105082921515X-RAY DIFFRACTION99.7581620314
2.6466-2.7670.3335665217611480.2357611820561489X-RAY DIFFRACTION99.4532199271
2.767-2.91270.2786809093051340.2401824302781492X-RAY DIFFRACTION99.0859232176
2.9127-3.0950.3249232965271520.2440329546681487X-RAY DIFFRACTION99.0332326284
3.095-3.33360.3049510424781400.2432548100171485X-RAY DIFFRACTION98.3656174334
3.3336-3.66850.2543914119791360.212973447961484X-RAY DIFFRACTION97.6491862568
3.6685-4.19780.2439078689851390.2063269039861491X-RAY DIFFRACTION96.7359050445
4.1978-5.28310.2176966494791410.1864921045111497X-RAY DIFFRACTION96.1267605634
5.2831-100.2337665093381480.2263765875071470X-RAY DIFFRACTION89.9388549194
Refinement TLS params.Method: refined / Origin x: -15.4034849429 Å / Origin y: 33.8495251343 Å / Origin z: -26.0303870789 Å
111213212223313233
T0.367436861635 Å2-0.00508629854779 Å20.0382570916331 Å2-0.357756141373 Å2-0.0110991269064 Å2--0.38347839272 Å2
L1.16440346815 °20.031546059216 °20.839368081547 °2-0.866227797161 °2-0.546541080774 °2--2.03107107278 °2
S-0.0329615761603 Å °0.0471258755941 Å °0.122454671775 Å °-0.0510656915469 Å °-0.0933280656001 Å °-0.11900112014 Å °-0.00696219274368 Å °0.133205980511 Å °0.124613385242 Å °
Refinement TLS groupSelection details: all

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