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- PDB-5lsj: CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEA... -

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Basic information

Entry
Database: PDB / ID: 5lsj
TitleCRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEAD2 COMPLEX
Components
  • Centromere protein C
  • Kinetochore-associated protein DSN1 homolog
  • Kinetochore-associated protein NSL1 homolog
  • 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 / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region ...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 / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / inner 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 speck / nuclear body / 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 / MOLECULAR REPLACEMENT / Resolution: 3.25 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
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: Protein MIS12 homolog
B: Polyamine-modulated factor 1
D: Kinetochore-associated protein DSN1 homolog
N: Kinetochore-associated protein NSL1 homolog
P: Centromere protein C
C: Protein MIS12 homolog
E: Polyamine-modulated factor 1
F: Kinetochore-associated protein DSN1 homolog
G: Kinetochore-associated protein NSL1 homolog
Q: Centromere protein C


Theoretical massNumber of molelcules
Total (without water)173,55810
Polymers173,55810
Non-polymers00
Water00
1
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)86,7795
Polymers86,7795
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24050 Å2
ΔGint-225 kcal/mol
Surface area31550 Å2
MethodPISA
2
C: Protein MIS12 homolog
E: Polyamine-modulated factor 1
F: Kinetochore-associated protein DSN1 homolog
G: Kinetochore-associated protein NSL1 homolog
Q: Centromere protein C


Theoretical massNumber of molelcules
Total (without water)86,7795
Polymers86,7795
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24260 Å2
ΔGint-223 kcal/mol
Surface area31860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.160, 156.400, 76.000
Angle α, β, γ (deg.)90.000, 102.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein MIS12 homolog


Mass: 24170.922 Da / Num. of mol.: 2
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.: 2 / 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
#3: Protein Kinetochore-associated protein DSN1 homolog


Mass: 20252.930 Da / Num. of mol.: 2 / Fragment: UNP residues 186-356
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: 13331.376 Da / Num. of mol.: 2 / Fragment: UNP residues 92-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSL1, C1orf48, DC31, DC8, MIS14 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q96IY1
#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.: 2 / Fragment: UNP residues 1-71
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPC, CENPC1, ICEN7 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q03188

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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: 2.9 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3→45.5 Å / Num. obs: 31073 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 23.7 % / Biso Wilson estimate: 48.372 Å2 / Rmerge(I) obs: 0.351 / Net I/σ(I): 9.47
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3-3.0824.821.0263.891100
3.08-3.160.9784.11100
3.16-3.250.9494.21199.8
3.25-3.350.8684.731100
3.35-3.460.8145.11199.8
3.46-3.590.735.63199.8
3.59-3.720.6096.851100
3.72-3.870.5357.47199.8
3.87-4.050.4438.37199.9
4.05-4.240.3639.69199.9
4.24-4.470.32311.31100
4.47-4.740.27613.03199.4
4.74-5.070.24413.95199.7
5.07-5.480.27113.32199.9
5.48-60.30812.09199.9
6-6.710.29412.861100
6.71-7.750.18217.49199.5
7.75-9.490.11426.741100
9.49-13.420.09133.561100
13.420.08532.6196

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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: 3.25→19.993 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 34.34
RfactorNum. reflection% reflection
Rfree0.2971 1214 5 %
Rwork0.2463 --
obs0.2488 24286 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.63 Å2 / Biso mean: 54.8084 Å2 / Biso min: 10.91 Å2
Refinement stepCycle: LAST / Resolution: 3.25→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9621 0 0 0 9621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049773
X-RAY DIFFRACTIONf_angle_d0.81513140
X-RAY DIFFRACTIONf_chiral_restr0.0441461
X-RAY DIFFRACTIONf_plane_restr0.0051708
X-RAY DIFFRACTIONf_dihedral_angle_d19.8466097
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.25-3.37950.42551340.354425482682100
3.3795-3.53260.3771360.31725652701100
3.5326-3.71770.31311330.269525502683100
3.7177-3.94890.29851350.251225702705100
3.9489-4.25110.34661350.24192559269499
4.2511-4.6740.27581340.2242553268799
4.674-5.3390.28171350.22642554268999
5.339-6.68460.30141350.261125732708100
6.6846-19.99330.21191370.187226002737100

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