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- PDB-8yhh: The Crystal Structure of Mitotic Kinesin Eg5 from Biortus -

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Basic information

Entry
Database: PDB / ID: 8yhh
TitleThe Crystal Structure of Mitotic Kinesin Eg5 from Biortus
ComponentsKinesin-like protein KIF11
KeywordsCELL CYCLE / Motor protein / Cell division / ATP-binding
Function / homology
Function and homology information


spindle elongation / regulation of mitotic centrosome separation / plus-end-directed microtubule motor activity / Kinesins / mitotic centrosome separation / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / plus-end-directed microtubule motor activity / Kinesins / mitotic centrosome separation / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / spindle / spindle pole / mitotic spindle / mitotic cell cycle / microtubule binding / microtubule / ciliary basal body / cell division / intracellular membrane-bounded organelle / protein kinase binding / protein-containing complex / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / 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-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / 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 / NITRATE ION / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Qi, J. / Wu, B.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of Mitotic Kinesin Eg5 from Biortus
Authors: Wang, F. / Cheng, W. / Lv, Z. / Qi, J. / Wu, B.
History
DepositionFeb 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein KIF11
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,08817
Polymers82,3392
Non-polymers1,74915
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-39 kcal/mol
Surface area29370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.654, 78.254, 93.467
Angle α, β, γ (deg.)90.000, 94.511, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 17 - 364 / Label seq-ID: 19 - 366

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Kinesin-like protein KIF11 / Kinesin-like protein 1 / Kinesin-like spindle protein HKSP / Kinesin-related motor protein Eg5 / ...Kinesin-like protein 1 / Kinesin-like spindle protein HKSP / Kinesin-related motor protein Eg5 / Thyroid receptor-interacting protein 5 / TR-interacting protein 5 / TRIP-5


Mass: 41169.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52732

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Non-polymers , 7 types, 347 molecules

#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
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 19% PEG3350, 0.1M MES (pH 5.2), and 200 mM NaNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.95→46.59 Å / Num. obs: 51970 / % possible obs: 96.1 % / Redundancy: 5.4 % / CC1/2: 0.999 / Net I/σ(I): 13.7
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 3726 / CC1/2: 0.806

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.59 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.671 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / ESU R: 0.191 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2605 2409 4.637 %
Rwork0.2142 49540 -
all0.216 --
obs-51949 95.875 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.48 Å2
Baniso -1Baniso -2Baniso -3
1-3.737 Å2-0 Å2-1.029 Å2
2---1.502 Å2-0 Å2
3----2.047 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4983 0 110 332 5425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135217
X-RAY DIFFRACTIONr_bond_other_d0.0010.0145080
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.6547031
X-RAY DIFFRACTIONr_angle_other_deg1.1361.5811716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08621.573267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56215955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0111543
X-RAY DIFFRACTIONr_chiral_restr0.050.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021130
X-RAY DIFFRACTIONr_nbd_refined0.1840.2931
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.24657
X-RAY DIFFRACTIONr_nbtor_refined0.1430.22412
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.22628
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2338
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.226
X-RAY DIFFRACTIONr_nbd_other0.1680.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.210
X-RAY DIFFRACTIONr_mcbond_it1.993.9612552
X-RAY DIFFRACTIONr_mcbond_other1.993.9592551
X-RAY DIFFRACTIONr_mcangle_it3.2115.9153180
X-RAY DIFFRACTIONr_mcangle_other3.2115.9173181
X-RAY DIFFRACTIONr_scbond_it2.1074.3742665
X-RAY DIFFRACTIONr_scbond_other2.1074.3762663
X-RAY DIFFRACTIONr_scangle_it3.496.4183843
X-RAY DIFFRACTIONr_scangle_other3.4896.4193841
X-RAY DIFFRACTIONr_lrange_it5.91246.6195591
X-RAY DIFFRACTIONr_lrange_other5.84846.4585532
X-RAY DIFFRACTIONr_ncsr_local_group_10.0940.059621
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.093880.05008
12BX-RAY DIFFRACTIONLocal ncs0.093880.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3061700.3123746X-RAY DIFFRACTION97.8755
2.001-2.0550.2831690.2873649X-RAY DIFFRACTION98.3514
2.055-2.1150.2681760.2523516X-RAY DIFFRACTION98.3222
2.115-2.180.2811500.2373457X-RAY DIFFRACTION97.2237
2.18-2.2520.271400.2323269X-RAY DIFFRACTION95.8392
2.252-2.330.2771530.2313114X-RAY DIFFRACTION95.8064
2.33-2.4180.2111490.2053081X-RAY DIFFRACTION96.9388
2.418-2.5170.2721600.222907X-RAY DIFFRACTION95.754
2.517-2.6290.311440.2232776X-RAY DIFFRACTION94.8976
2.629-2.7570.281270.2122740X-RAY DIFFRACTION96.4995
2.757-2.9060.271150.2152545X-RAY DIFFRACTION96.1677
2.906-3.0820.2681460.2032395X-RAY DIFFRACTION96.1044
3.082-3.2950.2531320.2012267X-RAY DIFFRACTION95.6921
3.295-3.5580.297990.222117X-RAY DIFFRACTION95.189
3.558-3.8970.287770.2021930X-RAY DIFFRACTION93.7412
3.897-4.3570.242820.1881703X-RAY DIFFRACTION91.8682
4.357-5.0290.228840.1761506X-RAY DIFFRACTION93.3099
5.029-6.1540.227510.2121293X-RAY DIFFRACTION91.6155
6.154-8.6850.245490.206990X-RAY DIFFRACTION90.9011
8.685-46.590.194360.225539X-RAY DIFFRACTION89.5639

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