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- PDB-6m4i: Structure of CENP-E motor domain at 1.9 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6m4i
TitleStructure of CENP-E motor domain at 1.9 angstrom resolution
ComponentsCentromere-associated protein E
KeywordsCELL CYCLE / kinesin / motor domain / adp binding
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
ADENOSINE-5'-DIPHOSPHATE / Centromere-associated protein E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShibuya, A. / Yokoyama, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2021
Title: Structure and comparison of the motor domain ofcentromere-associated protein E
Authors: Shibuya, A. / Ogo, N. / Sawada, J. / Asai, A. / Yokoyama, H.
History
DepositionMar 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5016
Polymers79,5982
Non-polymers9034
Water2,522140
1
A: Centromere-associated protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2513
Polymers39,7991
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-17 kcal/mol
Surface area14780 Å2
MethodPISA
2
B: Centromere-associated protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2513
Polymers39,7991
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-16 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.825, 82.839, 49.372
Angle α, β, γ (deg.)90.000, 100.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 4 - 339 / Label seq-ID: 10 - 345

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 39799.082 Da / Num. of mol.: 2 / Fragment: Kinesin motor
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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsSequence conflict A300P is based on reference CAA78727 (Pubmed 1406971).

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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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Tris-HCl (pH 7.5), PEG 3350, PIPES-NaOH (pH 6.8), NaCl, MgCl2, EGTA-NaOH, TCEP, sucrose, CENP-E, CIBA

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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: May 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→95.095 Å / Num. all: 60258 / Num. obs: 60258 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Rsym value: 0.048 / Net I/av σ(I): 7.9 / Net I/σ(I): 18.2 / Num. measured all: 414345
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-270.830.96114987180.3370.8970.832.699.8
2-2.126.70.4351.75579283020.1810.4720.4354.399.8
2.12-2.276.70.2612.95232078030.1090.2840.2616.499.8
2.27-2.457.20.1774.35275372970.0710.190.1779.499.9
2.45-2.697.10.1066.94721066900.0430.1150.10614100
2.69-36.70.06610.44088760630.0270.0710.06620.8100
3-3.476.70.03914.73616253900.0160.0420.03934.4100
3.47-4.257.10.03118.43228445220.0120.0330.03148.7100
4.25-6.016.50.02920.12321335570.0120.0310.02953100
6.01-19.9166.60.03413.61257519160.0140.0370.03454.797

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALAdata scaling
Coot0.8.9.2model building
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5C

1t5c


Resolution: 1.9→19.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.497 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 6020 10 %RANDOM
Rwork0.2172 ---
obs0.2209 54214 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.54 Å2 / Biso mean: 55.785 Å2 / Biso min: 24.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.9→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4848 0 56 140 5044
Biso mean--53.09 50.56 -
Num. residues----609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135065
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174712
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6466846
X-RAY DIFFRACTIONr_angle_other_deg1.2991.57910931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2945611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60422.251271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11215910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0481535
X-RAY DIFFRACTIONr_chiral_restr0.0740.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021058
Refine LS restraints NCS

Ens-ID: 1 / Number: 9592 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 442 -
Rwork0.402 3948 -
all-4390 -
obs--99.84 %

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