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- PDB-5lsi: CRYSTAL STRUCTURE OF THE KINETOCHORE MIS12 COMPLEX HEAD2 SUBDOMAI... -

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Basic information

Entry
Database: PDB / ID: 5lsi
TitleCRYSTAL STRUCTURE OF THE KINETOCHORE MIS12 COMPLEX HEAD2 SUBDOMAIN CONTAINING DSN1 AND NSL1 FRAGMENTS
Components
  • Kinetochore-associated protein DSN1 homolog
  • Kinetochore-associated protein NSL1 homolog
KeywordsCELL CYCLE / ALPHA-HELICAL
Function / homology
Function and homology information


MIS12/MIND type complex / skeletal muscle satellite cell proliferation / attachment of spindle microtubules to kinetochore / outer kinetochore / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins ...MIS12/MIND type complex / skeletal muscle satellite cell proliferation / attachment of spindle microtubules to kinetochore / outer kinetochore / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / kinetochore / fibrillar center / spindle pole / Separation of Sister Chromatids / azurophil granule lumen / nuclear speck / nuclear body / cell division / Neutrophil degranulation / nucleolus / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Kinetochore Mis14/Nsl1 / Kinetochore protein Mis14 like / Kinetochore-associated protein Dsn1/Mis13 / Mis12-Mtw1 protein family
Similarity search - Domain/homology
Kinetochore-associated protein NSL1 homolog / Kinetochore-associated protein DSN1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsVetter, I.R. / Petrovic, A. / Keller, J. / Liu, Y.
CitationJournal: Cell / Year: 2016
Title: Structure of the MIS12 Complex and Molecular Basis of Its Interaction with CENP-C at Human Kinetochores.
Authors: Petrovic, A. / Keller, J. / Liu, Y. / Overlack, K. / John, J. / Dimitrova, Y.N. / Jenni, S. / van Gerwen, S. / Stege, P. / Wohlgemuth, S. / Rombaut, P. / Herzog, F. / Harrison, S.C. / ...Authors: Petrovic, A. / Keller, J. / Liu, Y. / Overlack, K. / John, J. / Dimitrova, Y.N. / Jenni, S. / van Gerwen, S. / Stege, P. / Wohlgemuth, S. / Rombaut, P. / Herzog, F. / Harrison, S.C. / Vetter, I.R. / Musacchio, A.
History
DepositionSep 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jan 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

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Assembly

Deposited unit
D: Kinetochore-associated protein DSN1 homolog
E: Kinetochore-associated protein NSL1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8973
Polymers23,8012
Non-polymers961
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-41 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.640, 59.640, 82.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Kinetochore-associated protein DSN1 homolog


Mass: 15313.180 Da / Num. of mol.: 1 / Fragment: head2 domain, UNP residues 68-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DSN1, C20orf172, MIS13 / Plasmid: pGEX-2rbs / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q9H410
#2: Protein Kinetochore-associated protein NSL1 homolog


Mass: 8487.469 Da / Num. of mol.: 1 / Fragment: UNP residues 29-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSL1, C1orf48, DC31, DC8, MIS14 / Plasmid: pGEX-2rbs / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q96IY1
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 48.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 2M ammonium sulfate, 0.2M potassium sodium phosphate, 0.1M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→43.754 Å / Num. obs: 11845 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 19.1 % / Biso Wilson estimate: 34.67 Å2 / Rmerge(I) obs: 0.242 / Net I/σ(I): 10.63
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.0518.11.3552.12199.4
2.05-2.111.2922.581100
2.11-2.171.1632.951100
2.17-2.241.1023.211100
2.24-2.311.0113.561100
2.31-2.390.94.211100
2.39-2.480.8264.74199.9
2.48-2.580.765.181100
2.58-2.70.6286.3199.8
2.7-2.830.5427.251100
2.83-2.980.4229.291100
2.98-3.170.31211.82199.8
3.17-3.380.22516.141100
3.38-3.660.15920.561100
3.66-40.11226.67199.8
4-4.480.08931.881100
4.48-5.170.08730.341100
5.17-6.330.10426.831100
6.33-8.950.06435.491100
8.950.04641.65199.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LSK

5lsk


Resolution: 2.002→43.754 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.12
RfactorNum. reflection% reflection
Rfree0.2458 593 5.01 %
Rwork0.2158 --
obs0.2173 11837 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.18 Å2 / Biso mean: 40.5025 Å2 / Biso min: 18.67 Å2
Refinement stepCycle: LAST / Resolution: 2.002→43.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 5 53 1288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031252
X-RAY DIFFRACTIONf_angle_d0.5161682
X-RAY DIFFRACTIONf_chiral_restr0.037185
X-RAY DIFFRACTIONf_plane_restr0.003221
X-RAY DIFFRACTIONf_dihedral_angle_d16.916764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0021-2.20360.31471450.290127562901
2.2036-2.52240.28911460.239827552901
2.5224-3.17780.23871480.224428112959
3.1778-43.76460.22151540.189129223076

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