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- PDB-8hfh: CENP-E motor domain in complex with AMPPNP and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 8hfh
TitleCENP-E motor domain in complex with AMPPNP and Mg2+
ComponentsCentromere-associated protein E
KeywordsCELL CYCLE / kinesin / motor domain / AMPPNP / CENP-E / centromere-associated protein
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 / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region ...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 / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / 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 / mitotic cell cycle / chromosome / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IMIDAZOLE / Centromere-associated protein E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsShibuya, A. / Yokoyama, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Febs Lett. / Year: 2023
Title: Crystal structure of the motor domain of centromere-associated protein E in complex with a non-hydrolysable ATP analogue.
Authors: Shibuya, A. / Suzuki, A. / Ogo, N. / Sawada, J.I. / Asai, A. / Yokoyama, H.
History
DepositionNov 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centromere-associated protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4687
Polymers39,7991
Non-polymers6696
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration data suggests that CENP-E motor domain is monomeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.576, 46.215, 73.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-602-

NA

21A-605-

IMD

31A-710-

HOH

41A-735-

HOH

51A-976-

HOH

61A-986-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 39799.082 Da / Num. of mol.: 1 / Mutation: A300P
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

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Non-polymers , 5 types, 308 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MES, PEG3350, PIPES-NaOH, NaCl, MgCl2, EGTA, TCEP, sucrose, CENP-E, AMPPNP

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→73.718 Å / Num. obs: 31976 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.6 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.119 / Rsym value: 0.11 / Net I/av σ(I): 6.1 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.94.20.5011.545880.2730.5730.50199.8
1.9-2.016.60.374243630.1560.4060.374100
2.01-2.156.90.2772.640920.1130.30.277100
2.15-2.326.70.2043.538300.0840.2210.204100
2.32-2.556.50.1574.535400.0670.1710.157100
2.55-2.856.90.1225.832230.050.1320.122100
2.85-3.296.60.085828650.0360.0920.085100
3.29-4.026.40.05611.924260.0240.0610.056100
4.02-5.696.70.04813.119460.020.0520.048100
5.69-105.80.04314.311030.0190.0470.04397.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.572
Highest resolutionLowest resolution
Rotation19.86 Å1.88 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M4I

6m4i


Resolution: 1.8→19.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.452 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 3149 9.9 %RANDOM
Rwork0.1611 ---
obs0.1654 28790 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.84 Å2 / Biso mean: 18.794 Å2 / Biso min: 3.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 40 302 2887
Biso mean--17.05 29.67 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132647
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152532
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6523575
X-RAY DIFFRACTIONr_angle_other_deg1.4441.5835820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25821.972142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05815481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.71520
X-RAY DIFFRACTIONr_chiral_restr0.0870.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 242 -
Rwork0.243 2079 -
all-2321 -
obs--99.66 %

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