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- PDB-5lsk: CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C COMPLEX -

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Basic information

Entry
Database: PDB / ID: 5lsk
TitleCRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C COMPLEX
Components
  • (Kinetochore-associated protein ...) x 2
  • Centromere protein C
  • Polyamine-modulated factor 1
  • Protein MIS12 homolog
KeywordsCELL CYCLE / ALPHA-HELICAL
Function / homology
Function and homology information


MIS12/MIND type complex / skeletal muscle satellite cell proliferation / leucine zipper domain binding / spindle attachment to meiosis I kinetochore / attachment of spindle microtubules to kinetochore / centromeric DNA binding / kinetochore assembly / inner kinetochore / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore ...MIS12/MIND type complex / skeletal muscle satellite cell proliferation / leucine zipper domain binding / spindle attachment to meiosis I kinetochore / attachment of spindle microtubules to kinetochore / centromeric DNA binding / kinetochore assembly / inner kinetochore / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / mitotic sister chromatid segregation / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / kinetochore / fibrillar center / spindle pole / Separation of Sister Chromatids / azurophil granule lumen / mitotic cell cycle / midbody / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / nuclear body / nuclear speck / cell division / intracellular membrane-bounded organelle / Neutrophil degranulation / nucleolus / Golgi apparatus / DNA binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Kinetochore Mis14/Nsl1 / Kinetochore protein Mis14 like / Nuclear MIS12/MIND complex subunit PMF1/Nnf1 / Centromere protein Mis12 / Nnf1 / Mis12 protein / Kinetochore-associated protein Dsn1/Mis13 / Mis12-Mtw1 protein family / CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region ...Kinetochore Mis14/Nsl1 / Kinetochore protein Mis14 like / Nuclear MIS12/MIND complex subunit PMF1/Nnf1 / Centromere protein Mis12 / Nnf1 / Mis12 protein / Kinetochore-associated protein Dsn1/Mis13 / Mis12-Mtw1 protein family / CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / 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
Centromere protein C / Polyamine-modulated factor 1 / Kinetochore-associated protein NSL1 homolog / Protein MIS12 homolog / Kinetochore-associated protein DSN1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.502 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 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein MIS12 homolog
B: Polyamine-modulated factor 1
D: Kinetochore-associated protein DSN1 homolog
N: Kinetochore-associated protein NSL1 homolog
P: Centromere protein C


Theoretical massNumber of molelcules
Total (without water)110,3515
Polymers110,3515
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28980 Å2
ΔGint-264 kcal/mol
Surface area42550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.010, 112.690, 90.810
Angle α, β, γ (deg.)90.000, 114.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABP

#1: Protein Protein MIS12 homolog


Mass: 24170.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIS12 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q9H081
#2: Protein Polyamine-modulated factor 1 / PMF-1


Mass: 20522.359 Da / Num. of mol.: 1 / Fragment: UNP residues 31-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMF1 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q6P1K2
#5: Protein Centromere protein C / CENP-C / Centromere autoantigen C / Centromere protein C 1 / CENP-C 1 / Interphase centromere ...CENP-C / Centromere autoantigen C / Centromere protein C 1 / CENP-C 1 / Interphase centromere complex protein 7


Mass: 8501.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPC, CENPC1, ICEN7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q03188

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Kinetochore-associated protein ... , 2 types, 2 molecules DN

#3: Protein Kinetochore-associated protein DSN1 homolog


Mass: 33848.191 Da / Num. of mol.: 1 / Fragment: UNP residues 68-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DSN1, C20orf172, MIS13 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q9H410
#4: Protein Kinetochore-associated protein NSL1 homolog


Mass: 23307.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSL1, C1orf48, DC31, DC8, MIS14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q96IY1

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Non-polymers , 1 types, 6 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.9 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 6-12% PEG6000 / PH range: 6-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97863 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97863 Å / Relative weight: 1
ReflectionResolution: 3.5→19.742 Å / Num. obs: 16932 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.76 % / Biso Wilson estimate: 98.247 Å2 / Rmerge(I) obs: 0.181 / Net I/σ(I): 7.16
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.5-3.591.9561.05199.1
3.59-3.691.5921.33199.4
3.69-3.81.0482.041100
3.8-3.910.8292.46199.4
3.91-4.040.5873.35199.7
4.04-4.180.4614.03199.5
4.18-4.340.3425.21100
4.34-4.520.2695.9199.7
4.52-4.720.2137.04199.4
4.72-4.950.1827.81199.8
4.95-5.220.1718.75199.3
5.22-5.530.1938.1199.6
5.53-5.920.2437.54199.7
5.92-6.390.2278.42199.3
6.39-70.17110.51199.7
7-7.830.09915.39199.3
7.83-9.040.06621.88199.8
9.04-11.070.05326.21199.6
11.07-15.650.0527.09197
15.650.0528.52149

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.502→19.742 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.84
RfactorNum. reflection% reflection
Rfree0.2977 712 5.02 %
Rwork0.2444 --
obs0.2471 14170 83.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 167.51 Å2 / Biso mean: 74.2897 Å2 / Biso min: 22.94 Å2
Refinement stepCycle: LAST / Resolution: 3.502→19.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6186 0 0 6 6192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026282
X-RAY DIFFRACTIONf_angle_d0.638443
X-RAY DIFFRACTIONf_chiral_restr0.037937
X-RAY DIFFRACTIONf_plane_restr0.0031100
X-RAY DIFFRACTIONf_dihedral_angle_d18.3023909
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5024-3.77110.3492690.31941279134840
3.7711-4.14740.37351250.27962553267880
4.1474-4.74030.33341680.253631843352100
4.7403-5.94510.30381840.267931973381100
5.9451-19.74260.22861660.193432453411100

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