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- PDB-6l80: Crystal structure of pombe Mod21 N-terminus and Mozart1 -

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Basic information

Entry
Database: PDB / ID: 6l80
TitleCrystal structure of pombe Mod21 N-terminus and Mozart1
Components
  • Gamma-tubulin complex subunit mod21
  • Mitotic-spindle organizing protein 1
KeywordsTRANSLATION / gamma tubulin complex / microprotien / microtubule
Function / homology
Function and homology information


spindle pole body anchor activity / inner plaque of mitotic spindle pole body / equatorial microtubule organizing center / microtubule nucleation by spindle pole body / gamma-tubulin small complex / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / mitotic spindle pole body / interphase microtubule organizing center / gamma-tubulin complex ...spindle pole body anchor activity / inner plaque of mitotic spindle pole body / equatorial microtubule organizing center / microtubule nucleation by spindle pole body / gamma-tubulin small complex / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / mitotic spindle pole body / interphase microtubule organizing center / gamma-tubulin complex / gamma-tubulin ring complex / microtubule nucleation / gamma-tubulin binding / mitotic spindle assembly / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle / spindle / mitotic cell cycle / microtubule / nucleus / cytoplasm / cytosol
Similarity search - Function
Gamma-Tubulin ring complex non-core subunit mod21, C-terminal / Gamma-tubulin complex subunit Mod21 / Gamma-Tubulin ring complex non-core subunit mod21, N-terminal / Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated
Similarity search - Domain/homology
Mitotic-spindle organizing protein 1 / Gamma-tubulin complex subunit mod21
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.00049753238 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 3, 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 subunit mod21
B: Mitotic-spindle organizing protein 1
C: Gamma-tubulin complex subunit mod21
D: Mitotic-spindle organizing protein 1


Theoretical massNumber of molelcules
Total (without water)48,4924
Polymers48,4924
Non-polymers00
Water1,58588
1
A: Gamma-tubulin complex subunit mod21
B: Mitotic-spindle organizing protein 1


Theoretical massNumber of molelcules
Total (without water)24,2462
Polymers24,2462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-40 kcal/mol
Surface area8750 Å2
MethodPISA
2
C: Gamma-tubulin complex subunit mod21
D: Mitotic-spindle organizing protein 1


Theoretical massNumber of molelcules
Total (without water)24,2462
Polymers24,2462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-43 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.513, 83.513, 122.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Gamma-tubulin complex subunit mod21


Mass: 12937.141 Da / Num. of mol.: 2 / Fragment: N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mod21, SPAC806.08c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UT52
#2: Protein Mitotic-spindle organizing protein 1


Mass: 11308.884 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mzt1, tam4, SPAC9G1.15c / Production host: Escherichia coli (E. coli) / References: UniProt: P0CF96*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFirst 3 residues (G,P, and H) from the provided sequence of chain B/D are expression tag of the protein.

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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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% v/v Tacsimate pH 7.0, 0.1 M Bis-Tris propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 267023 / % possible obs: 99.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 23.3077560766 Å2 / CC1/2: 0.995 / Net I/σ(I): 23.1
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 29883 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.00049753238→29.5263043086 Å / SU ML: 0.208899365849 / Cross valid method: FREE R-VALUE / σ(F): 1.33785732234 / Phase error: 22.6560892751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234597403669 3723 6.70122576813 %
Rwork0.199550446775 51834 -
obs0.201863724302 55557 99.1717391692 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.0801219207 Å2
Refinement stepCycle: LAST / Resolution: 2.00049753238→29.5263043086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 0 88 2603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007358168168792540
X-RAY DIFFRACTIONf_angle_d0.7632882810843416
X-RAY DIFFRACTIONf_chiral_restr0.0456171121532419
X-RAY DIFFRACTIONf_plane_restr0.00450150300664426
X-RAY DIFFRACTIONf_dihedral_angle_d18.43087809281591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0005-2.02580.2769362841761210.2498295613981696X-RAY DIFFRACTION86.9377990431
2.0258-2.05250.2335679413041330.2224119499511847X-RAY DIFFRACTION94.964028777
2.0525-2.08060.2946614802821360.2044074882591910X-RAY DIFFRACTION98.9361702128
2.0806-2.11030.2666675282641410.2073801114131938X-RAY DIFFRACTION99.9519230769
2.1103-2.14180.2300832803161350.2056893590591937X-RAY DIFFRACTION99.9035679846
2.1418-2.17520.2287478871311380.2060937571481891X-RAY DIFFRACTION100
2.1752-2.21090.2412328367311380.2031260056871958X-RAY DIFFRACTION99.8570747975
2.2109-2.2490.2603591296191430.2209932658111917X-RAY DIFFRACTION99.6131528046
2.249-2.28990.2379431833591360.2123870960071907X-RAY DIFFRACTION99.6585365854
2.2899-2.33390.2686871600491420.2140568195951958X-RAY DIFFRACTION99.9524036173
2.3339-2.38150.2164769687111340.1984662514651920X-RAY DIFFRACTION99.9513381995
2.3815-2.43330.2457321074931420.2056470901851951X-RAY DIFFRACTION100
2.4333-2.48990.3133437800521370.2059948547941943X-RAY DIFFRACTION99.9519461797
2.4899-2.55210.2715221152081360.2236077412551927X-RAY DIFFRACTION100
2.5521-2.62110.2228862598661420.2135601189051961X-RAY DIFFRACTION99.9524714829
2.6211-2.69810.2461200628011380.2027047183931930X-RAY DIFFRACTION99.8551424433
2.6981-2.78520.2567410851291400.2148025357381922X-RAY DIFFRACTION99.9031007752
2.7852-2.88460.2615552593881370.2313903028631945X-RAY DIFFRACTION100
2.8846-30.2734672644761410.2225006436991926X-RAY DIFFRACTION100
3-3.13640.2396487853441390.2049066743791906X-RAY DIFFRACTION99.9511241447
3.1364-3.30150.2438895492771370.2072460568721952X-RAY DIFFRACTION100
3.3015-3.50810.2430087338331390.1961256912141943X-RAY DIFFRACTION99.9040307102
3.5081-3.77850.2205779172491440.1822538985251931X-RAY DIFFRACTION100
3.7785-4.15780.1951946282991420.1645841591411928X-RAY DIFFRACTION99.9034749035
4.1578-4.75720.1910544609731330.1562892152951931X-RAY DIFFRACTION99.7101449275
4.7572-5.98540.2294468925681360.2004074365061935X-RAY DIFFRACTION99.9035214665
5.9854-100.1915305398771430.2007004206011924X-RAY DIFFRACTION99.1842610365
Refinement TLS params.Method: refined / Origin x: 41.8997806617 Å / Origin y: 41.3625837428 Å / Origin z: 47.1580100255 Å
111213212223313233
T0.19924547516 Å20.0203069110137 Å20.00231173212613 Å2-0.138916032396 Å20.00727000681086 Å2--0.119456756786 Å2
L1.18799673016 °2-0.0782198961305 °20.284372994866 °2-0.913790195479 °20.0166164500339 °2--1.18622267435 °2
S0.0488740097353 Å °0.266579052807 Å °0.000798094363958 Å °-0.253194550152 Å °-0.0668499004594 Å °-0.0331058068809 Å °0.0212372092123 Å °0.07198096842 Å °0.0146639954533 Å °
Refinement TLS groupSelection details: all

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