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

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Basic information

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


regulation of chromosome segregation / metaphase chromosome alignment / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / COPI-dependent Golgi-to-ER retrograde traffic ...regulation of chromosome segregation / metaphase chromosome alignment / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / COPI-dependent Golgi-to-ER retrograde traffic / 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 / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / chromosome, centromeric region / spindle / kinetochore / microtubule cytoskeleton / microtubule binding / microtubule / cell division / centrosome / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
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 / ALUMINUM FLUORIDE / Kinesin-like protein KIF2C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.43 Å
AuthorsOgawa, T. / Jiang, X. / Hirokawa, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)23000013, 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 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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

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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)97,9788
Polymers96,9072
Non-polymers1,0716
Water1267
1
A: Kinesin-like protein KIF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9894
Polymers48,4541
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area17120 Å2
MethodPISA
2
B: Kinesin-like protein KIF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9894
Polymers48,4541
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-6 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.098, 166.989, 74.991
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 183-585
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: potassium sodium tartrate tetrahydrate, MES, pH 6.0

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.43→30 Å / Num. obs: 15927 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.068 / Net I/σ(I): 11.9
Reflection shellResolution: 3.43→3.52 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1108 / Rpim(I) all: 0.273 / % 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: 1V8J

1v8j


Resolution: 3.43→30 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.896 / SU B: 21.466 / SU ML: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 846 5.3 %RANDOM
Rwork0.1976 ---
obs0.1994 15064 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.99 Å2 / Biso mean: 67.344 Å2 / Biso min: 26.58 Å2
Baniso -1Baniso -2Baniso -3
1-5.86 Å20 Å2-0 Å2
2---3.29 Å20 Å2
3----2.57 Å2
Refinement stepCycle: final / Resolution: 3.43→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 64 7 5339
Biso mean--51.51 33.06 -
Num. residues----669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195411
X-RAY DIFFRACTIONr_bond_other_d0.0070.025260
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9817278
X-RAY DIFFRACTIONr_angle_other_deg1.388312078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8295659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95823.583240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8321544
X-RAY DIFFRACTIONr_chiral_restr0.0930.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025981
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021241
LS refinement shellResolution: 3.43→3.519 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 61 -
Rwork0.272 1101 -
all-1162 -
obs--100 %

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