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- PDB-5mu3: Crystal structure of Ctf19-Mcm21 kinetochore assembly bound with ... -

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Basic information

Entry
Database: PDB / ID: 5mu3
TitleCrystal structure of Ctf19-Mcm21 kinetochore assembly bound with Ctf19-Mcm21 binding motif of central kinetochore subunit Okp1
Components
  • (Central kinetochore subunit CTF19) x 2
  • Central kinetochore subunit MCM21
  • Central kinetochore subunit Okp1
KeywordsCELL CYCLE / chromosome segregation / centromere / kinetochore / RWD domain
Function / homology
Function and homology information


centromere complex assembly / meiotic cell cycle / kinetochore / cell division / nucleus
Similarity search - Function
Rossmann fold - #12050 / Ctf19, second RWD domain / Ctf19, first RWD domain / Centromere protein O / Cenp-O kinetochore centromere component / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Inner kinetochore subunit OKP1 / Inner kinetochore subunit CTF19 / Inner kinetochore subunit MCM21
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchmitzberger, F.
Funding support Austria, United States, 2items
OrganizationGrant numberCountry
Boehringer Ingelheim Austria
Howard Hughes Medical Institute United States
Citation
Journal: EMBO J. / Year: 2017
Title: Molecular basis for inner kinetochore configuration through RWD domain-peptide interactions.
Authors: Schmitzberger, F. / Richter, M.M. / Gordiyenko, Y. / Robinson, C.V. / Dadlez, M. / Westermann, S.
#1: Journal: EMBO Rep. / Year: 2012
Title: RWD domain: a recurring module in kinetochore architecture shown by a Ctf19-Mcm21 complex structure.
Authors: Schmitzberger, F. / Harrison, S.C.
History
DepositionJan 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 21, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Central kinetochore subunit MCM21
B: Central kinetochore subunit CTF19
C: Central kinetochore subunit Okp1
D: Central kinetochore subunit MCM21
E: Central kinetochore subunit CTF19
F: Central kinetochore subunit Okp1


Theoretical massNumber of molelcules
Total (without water)97,4846
Polymers97,4846
Non-polymers00
Water6,089338
1
A: Central kinetochore subunit MCM21
B: Central kinetochore subunit CTF19
C: Central kinetochore subunit Okp1


Theoretical massNumber of molelcules
Total (without water)48,7343
Polymers48,7343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-38 kcal/mol
Surface area18960 Å2
MethodPISA
2
D: Central kinetochore subunit MCM21
E: Central kinetochore subunit CTF19
F: Central kinetochore subunit Okp1


Theoretical massNumber of molelcules
Total (without water)48,7503
Polymers48,7503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-36 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.342, 105.476, 122.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Central kinetochore subunit MCM21 / Minichromosome maintenance protein 21


Mass: 22071.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: MCM21, KLLA0B10142g / Plasmid: pET3aTR / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q6CVQ9
#2: Protein Central kinetochore subunit CTF19 / Chromosome transmission fidelity protein 19


Mass: 19046.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: CTF19, KLLA0D07612g / Plasmid: pET3aTR / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q6CRN7
#3: Protein Central kinetochore subunit Okp1 / Okp1


Mass: 7616.612 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: KLLA0_F15136g / Plasmid: pET3aTR / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q6CJY0
#4: Protein Central kinetochore subunit CTF19 / Chromosome transmission fidelity protein 19


Mass: 19062.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: CTF19, KLLA0D07612g / Plasmid: pET3aTR / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q6CRN7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 3.1 Å3/Da / Density % sol: 60 % / Description: Cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 35 % (v/v) glycerol ethoxylate 200 mM Li-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2014 / Details: Kirkpatrick-Baez mirrors
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→122.98 Å / Num. obs: 71441 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 45.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.073 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.4 % / Rmerge(I) obs: 3.446 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4549 / CC1/2: 0.192 / Rpim(I) all: 2.533 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSJanuary 2014data reduction
Aimless0.1.27data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZXU

3zxu


Resolution: 2.1→80.063 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 32.41
Details: maximum likelihood target with two-fold non-crystallographic symmetry restraints
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 3247 2.42 %Random selection
Rwork0.2217 ---
obs0.2223 71210 97.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→80.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6107 0 0 338 6445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026244
X-RAY DIFFRACTIONf_angle_d0.4568437
X-RAY DIFFRACTIONf_dihedral_angle_d8.6593778
X-RAY DIFFRACTIONf_chiral_restr0.041961
X-RAY DIFFRACTIONf_plane_restr0.0021066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13140.43951210.47584828X-RAY DIFFRACTION83
2.1314-2.16470.46371410.45095289X-RAY DIFFRACTION91
2.1647-2.20020.40351360.43055582X-RAY DIFFRACTION96
2.2002-2.23810.39941480.4015622X-RAY DIFFRACTION98
2.2381-2.27880.3331410.3835756X-RAY DIFFRACTION99
2.2788-2.32260.39091450.3545728X-RAY DIFFRACTION99
2.3226-2.370.33741410.33455750X-RAY DIFFRACTION100
2.37-2.42160.34151470.32435820X-RAY DIFFRACTION100
2.4216-2.47790.34981410.31695757X-RAY DIFFRACTION100
2.4779-2.53990.32731440.2965796X-RAY DIFFRACTION100
2.5399-2.60860.31041420.2755834X-RAY DIFFRACTION100
2.6086-2.68530.30131390.25835747X-RAY DIFFRACTION100
2.6853-2.7720.27431420.24935812X-RAY DIFFRACTION100
2.772-2.87110.30491490.23345791X-RAY DIFFRACTION100
2.8711-2.9860.23741400.22145753X-RAY DIFFRACTION100
2.986-3.1220.2591460.21135794X-RAY DIFFRACTION99
3.122-3.28660.26011440.21665779X-RAY DIFFRACTION99
3.2866-3.49250.25931430.19585764X-RAY DIFFRACTION99
3.4925-3.76210.21161380.17555786X-RAY DIFFRACTION99
3.7621-4.14070.17961370.1635727X-RAY DIFFRACTION99
4.1407-4.73980.17081390.15225763X-RAY DIFFRACTION99
4.7398-5.97140.18211420.18455734X-RAY DIFFRACTION99
5.9714-80.12130.2851410.23795673X-RAY DIFFRACTION97

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