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- PDB-5xjb: The Crystal Structure of the Minimal Core Domain of the Microtubu... -

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Basic information

Entry
Database: PDB / ID: 5xjb
TitleThe Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with ADP-Mg-BeFx
ComponentsKinesin-like protein KIF2C
KeywordsSTRUCTURAL PROTEIN / Kinesin / Microtubule / tubulin / KIF2 / MCAK / depolymerization
Function / homology
Function and homology information


postsynaptic cytoskeleton organization / regulation of chromosome segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / metaphase chromosome alignment / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / COPI-dependent Golgi-to-ER retrograde traffic ...postsynaptic cytoskeleton organization / regulation of chromosome segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / metaphase chromosome alignment / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / Separation of Sister Chromatids / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / MHC class II antigen presentation / microtubule plus-end binding / microtubule depolymerization / microtubule motor activity / microtubule-based movement / mitotic metaphase chromosome alignment / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / chromosome, centromeric region / kinetochore / presynapse / postsynapse / cell division / glutamatergic synapse / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / Kinesin-like protein KIF2A-like, N-terminal / 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 / BERYLLIUM TRIFLUORIDE ION / Kinesin-like protein KIF2C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsOgawa, T. / Jiang, X. / Hirokawa, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministriy of Education, Culture, Sports, Science and Technology23000013, 16H06372 Japan
CitationJournal: Cell Rep / Year: 2017
Title: Mechanism of Catalytic Microtubule Depolymerization via KIF2-Tubulin Transitional Conformation
Authors: Ogawa, T. / Saijo, S. / Shimizu, N. / Jiang, X. / Hirokawa, N.
History
DepositionApr 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,9428
Polymers96,9072
Non-polymers1,0356
Water905
1
A: Kinesin-like protein KIF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9714
Polymers48,4541
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-15 kcal/mol
Surface area17410 Å2
MethodPISA
2
B: Kinesin-like protein KIF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9714
Polymers48,4541
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-15 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.452, 166.593, 75.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 48453.543 Da / Num. of mol.: 2 / Fragment: UNP residues 184-585
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif2c / Production host: Escherichia coli (E. coli) / References: UniProt: Q922S8
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: potassium sodium tartrate tetrahydrate, MES, pH 6.0

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 21151 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Net I/σ(I): 23.2
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1561 / Rpim(I) all: 0.23 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V8K

1v8k


Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.892 / SU B: 19.877 / SU ML: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1061 5 %RANDOM
Rwork0.2012 ---
obs0.2042 20045 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: 172.98 Å2 / Biso mean: 79.629 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-10.25 Å20 Å2-0 Å2
2---6.08 Å20 Å2
3----4.17 Å2
Refinement stepCycle: final / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5275 0 64 5 5344
Biso mean--87.22 59.92 -
Num. residues----674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195422
X-RAY DIFFRACTIONr_bond_other_d0.0060.025292
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9827296
X-RAY DIFFRACTIONr_angle_other_deg1.27312147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9315666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54123.475236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92115996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7641545
X-RAY DIFFRACTIONr_chiral_restr0.0870.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026008
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021239
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 81 -
Rwork0.297 1433 -
all-1514 -
obs--100 %

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