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- PDB-4ubf: HsMCAK motor domain complex -

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Basic information

Entry
Database: PDB / ID: 4ubf
TitleHsMCAK motor domain complex
Components(Kinesin-like protein KIF2C) x 2
KeywordsCELL CYCLE / MCAK / Kif2c / Complex / Motor domain
Function / homology
Function and homology information


postsynaptic cytoskeleton organization / regulation of chromosome segregation / establishment or maintenance of microtubule cytoskeleton polarity / metaphase chromosome alignment / centromeric DNA binding / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / Kinesins / kinesin complex ...postsynaptic cytoskeleton organization / regulation of chromosome segregation / establishment or maintenance of microtubule cytoskeleton polarity / metaphase chromosome alignment / centromeric DNA binding / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / Kinesins / kinesin complex / microtubule depolymerization / microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic metaphase chromosome alignment / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / chromosome, centromeric region / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / kinetochore / spindle / Separation of Sister Chromatids / presynapse / microtubule cytoskeleton / microtubule binding / microtubule / postsynapse / cell division / centrosome / glutamatergic synapse / ATP hydrolysis activity / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / Kinesin-like protein KIF2A-like, N-terminal / Kinesin motor domain / Kinesin / 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-like protein KIF2A-like, N-terminal / Kinesin motor domain / Kinesin / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Kinesin-like protein KIF2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWelburn, J.P.I. / Talapatra, S.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK543WJW_R42094 United Kingdom
CitationJournal: Elife / Year: 2015
Title: The C-terminal region of the motor protein MCAK controls its structure and activity through a conformational switch.
Authors: Talapatra, S.K. / Harker, B. / Welburn, J.P.
History
DepositionAug 12, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein KIF2C
B: Kinesin-like protein KIF2C
C: Kinesin-like protein KIF2C
D: Kinesin-like protein KIF2C
P: Kinesin-like protein KIF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,43816
Polymers174,5595
Non-polymers1,87911
Water1,24369
1
A: Kinesin-like protein KIF2C
B: Kinesin-like protein KIF2C
P: Kinesin-like protein KIF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9199
Polymers87,9683
Non-polymers9526
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Kinesin-like protein KIF2C
D: Kinesin-like protein KIF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5197
Polymers86,5912
Non-polymers9275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.306, 245.644, 79.399
Angle α, β, γ (deg.)90.00, 95.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Kinesin-like protein KIF2C / Kinesin-like protein 6 / Mitotic centromere-associated kinesin / MCAK


Mass: 43295.602 Da / Num. of mol.: 4 / Fragment: UNP Residues 225-593
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2C, KNSL6 / Details (production host): pET28a-LIC / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q99661
#2: Protein/peptide Kinesin-like protein KIF2C / Kinesin-like protein 6 / Mitotic centromere-associated kinesin / MCAK


Mass: 1376.450 Da / Num. of mol.: 1 / Fragment: UNP Residues 709-720
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2C, KNSL6 / Plasmid: pET28a-LIC / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q99661
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Mg / Source: (natural) Homo sapiens (human)
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.94 % / Description: Single Rectangular Crystal
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 24 % w/v PEG 1500 20 % v/v Glycerol Protein crystals appeared after two days and single crystals were used for measurement
Temp details: Controlled Temperature Room

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 155983 / Num. obs: 35146 / % possible obs: 99.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.2
Reflection shellResolution: 3→3.5 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HEH

2heh


Resolution: 3→29.492 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2863 1746 5.01 %Random Selection
Rwork0.264 ---
obs0.2652 34816 99.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9506 0 115 69 9690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069989
X-RAY DIFFRACTIONf_angle_d1.22713505
X-RAY DIFFRACTIONf_dihedral_angle_d18.8743565
X-RAY DIFFRACTIONf_chiral_restr0.081593
X-RAY DIFFRACTIONf_plane_restr0.0051683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.08820.39931300.34072802X-RAY DIFFRACTION98
3.0882-3.18780.38831290.33882721X-RAY DIFFRACTION99
3.1878-3.30150.37621250.34012813X-RAY DIFFRACTION99
3.3015-3.43350.36291370.31472720X-RAY DIFFRACTION100
3.4335-3.58960.34361530.29322785X-RAY DIFFRACTION100
3.5896-3.77840.2741550.28582737X-RAY DIFFRACTION99
3.7784-4.01460.31451610.27642742X-RAY DIFFRACTION99
4.0146-4.32370.27011320.25072757X-RAY DIFFRACTION99
4.3237-4.75720.25051540.2242713X-RAY DIFFRACTION98
4.7572-5.44180.28771540.24952735X-RAY DIFFRACTION99
5.4418-6.8420.28041790.28012745X-RAY DIFFRACTION99
6.842-29.49320.22971370.21892800X-RAY DIFFRACTION99

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