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- PDB-8owi: Crystal structure of the corona-targeting domain of CENP-E -

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Basic information

Entry
Database: PDB / ID: 8owi
TitleCrystal structure of the corona-targeting domain of CENP-E
ComponentsCentromere-associated protein E
KeywordsCELL CYCLE / Kinesin motor / kinetochores / microtubules / mitosis
Function / homology
Function and homology information


lateral attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end directed mitotic chromosome migration / mitotic chromosome movement towards spindle pole / metaphase chromosome alignment / mitotic spindle midzone / kinetochore microtubule / kinetochore binding / kinetochore assembly / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore ...lateral attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end directed mitotic chromosome migration / mitotic chromosome movement towards spindle pole / metaphase chromosome alignment / mitotic spindle midzone / kinetochore microtubule / kinetochore binding / kinetochore assembly / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / Kinesins / regulation of mitotic metaphase/anaphase transition / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / mitotic metaphase chromosome alignment / intercellular bridge / microtubule-based movement / chromosome, centromeric region / positive regulation of protein kinase activity / spindle midzone / 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 / MHC class II antigen presentation / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / mitotic spindle / kinetochore / Separation of Sister Chromatids / microtubule cytoskeleton / chromosome / mitotic cell cycle / midbody / microtubule binding / microtubule / cell division / intracellular membrane-bounded organelle / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Centromere-associated protein E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsLegal, T. / Davies, O.R. / Welburn, J.P.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust219413/Z/19/Z United Kingdom
Wellcome Trust207430 United Kingdom
CitationJournal: Curr.Biol. / Year: 2024
Title: A conserved CENP-E region mediates BubR1-independent recruitment to the outer corona at mitotic onset.
Authors: Weber, J. / Legal, T. / Lezcano, A.P. / Gluszek-Kustusz, A. / Paterson, C. / Eibes, S. / Barisic, M. / Davies, O.R. / Welburn, J.P.I.
History
DepositionApr 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type
Revision 1.2Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centromere-associated protein E
B: Centromere-associated protein E


Theoretical massNumber of molelcules
Total (without water)34,7782
Polymers34,7782
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-24 kcal/mol
Surface area8750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.018, 84.018, 65.019
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11B-2624-

HOH

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Components

#1: Protein Centromere-associated protein E / Centromere protein E / CENP-E / Kinesin-7 / Kinesin-related protein CENPE


Mass: 17388.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPE / Production host: Escherichia coli (E. coli) / References: UniProt: Q02224
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Potassium citrate tribasic monohydrate pH 8.3, 20% w/v polyethene glycol 3,350, with 30% glycerol (cryoprotectant).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.14→51.42 Å / Num. obs: 9178 / % possible obs: 68.8 % / Redundancy: 24.8 % / Biso Wilson estimate: 36.9 Å2 / CC1/2: 1 / Rpim(I) all: 0.026 / Net I/σ(I): 17.9
Reflection shellResolution: 2.14→2.34 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 82 / CC1/2: 0.565 / Rpim(I) all: 0.563 / % possible all: 15

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Processing

Software
NameVersionClassification
autoPROCdata processing
PHENIX1.19.2_4158refinement
STARANISOdata scaling
Arcimboldophasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→51.42 Å / SU ML: 0.2013 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.4503
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2455 457 4.98 %
Rwork0.2161 8717 -
obs0.2176 9174 68.78 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.97 Å2
Refinement stepCycle: LAST / Resolution: 2.14→51.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 0 52 971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043921
X-RAY DIFFRACTIONf_angle_d0.57381216
X-RAY DIFFRACTIONf_chiral_restr0.0323139
X-RAY DIFFRACTIONf_plane_restr0.004152
X-RAY DIFFRACTIONf_dihedral_angle_d12.7008394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.450.2377460.2832894X-RAY DIFFRACTION21.7
2.45-3.090.26651780.25723460X-RAY DIFFRACTION82.76
3.09-51.420.23812330.19814363X-RAY DIFFRACTION99.76

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