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- PDB-5t59: Structure of the MIND Complex Shows a Regulatory Focus of Yeast K... -

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Basic information

Entry
Database: PDB / ID: 5t59
TitleStructure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly
Components
  • KLLA0B13629p
  • KLLA0E05809p
  • KLLA0F02343p
KeywordsCELL CYCLE / kinetochore / complex / chromosome / segregation / MIND / Mis12
Function / homology
Function and homology information


MIS12/MIND type complex / spindle attachment to meiosis I kinetochore / centromeric DNA binding / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / mitotic sister chromatid segregation / chromosome segregation / kinetochore / cell division / nucleus
Similarity search - Function
Kinetochore-associated protein Nnf1 / Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Nuclear MIS12/MIND complex subunit PMF1/Nnf1 / Centromere protein Mis12 / Nnf1 / Mis12 protein / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like ...Kinetochore-associated protein Nnf1 / Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Nuclear MIS12/MIND complex subunit PMF1/Nnf1 / Centromere protein Mis12 / Nnf1 / Mis12 protein / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
KLLA0F02343p / Kinetochore-associated protein / KLLA0B13629p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.405 Å
AuthorsDimitrova, Y. / Jenni, S. / Valverde, R. / Khin, Y. / Harrison, S.C.
CitationJournal: Cell / Year: 2016
Title: Structure of the MIND Complex Defines a Regulatory Focus for Yeast Kinetochore Assembly.
Authors: Dimitrova, Y.N. / Jenni, S. / Valverde, R. / Khin, Y. / Harrison, S.C.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Mar 6, 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

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Assembly

Deposited unit
A: KLLA0F02343p
B: KLLA0E05809p
C: KLLA0B13629p
D: KLLA0F02343p
E: KLLA0E05809p
F: KLLA0B13629p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0108
Polymers61,5966
Non-polymers4152
Water59433
1
A: KLLA0F02343p
B: KLLA0E05809p
C: KLLA0B13629p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0054
Polymers30,7983
Non-polymers2071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: KLLA0F02343p
E: KLLA0E05809p
F: KLLA0B13629p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0054
Polymers30,7983
Non-polymers2071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.400, 91.700, 95.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTrimer confirmed by gel filtration

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Components

#1: Protein KLLA0F02343p


Mass: 13870.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues Asn0 and Ala1 are left over from the TEV cleavage site. Mtw1 starts at residue Thr2.
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_F02343g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CLK3
#2: Protein KLLA0E05809p


Mass: 12100.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_E05809g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CPD1
#3: Protein/peptide KLLA0B13629p


Mass: 4826.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_B13629g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CVA1
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CHES, pH 9.0, 18-30 % PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.405→66.17 Å / Num. obs: 16798 / % possible obs: 56.5 % / Redundancy: 3.6 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.405→66.168 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.39
RfactorNum. reflection% reflection
Rfree0.2905 836 4.98 %
Rwork0.2492 --
obs0.2513 16798 63.61 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 2.405→66.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 26 33 3834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053852
X-RAY DIFFRACTIONf_angle_d0.6185180
X-RAY DIFFRACTIONf_dihedral_angle_d6.5243356
X-RAY DIFFRACTIONf_chiral_restr0.037591
X-RAY DIFFRACTIONf_plane_restr0.004660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.405-2.55570.4277140.375260X-RAY DIFFRACTION6
2.5557-2.75310.424460.3391926X-RAY DIFFRACTION22
2.7531-3.03010.3491280.32312368X-RAY DIFFRACTION57
3.0301-3.46860.30852040.30344093X-RAY DIFFRACTION98
3.4686-4.36990.25912190.23114113X-RAY DIFFRACTION98
4.3699-66.19260.28852250.21994202X-RAY DIFFRACTION96

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