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- PDB-2heh: Crystal Structure of the KIF2C motor domain -

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Basic information

Entry
Database: PDB / ID: 2heh
TitleCrystal Structure of the KIF2C motor domain
ComponentsKIF2C protein
KeywordsStructural genomics / structural protein / kinesin / motor domain / ADP / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


regulation of chromosome segregation / metaphase chromosome alignment / establishment or maintenance of microtubule cytoskeleton polarity / centromeric DNA binding / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule depolymerization ...regulation of chromosome segregation / metaphase chromosome alignment / establishment or maintenance of microtubule cytoskeleton polarity / centromeric DNA binding / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule depolymerization / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / chromosome, centromeric region / 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 / RHO GTPases Activate Formins / spindle / kinetochore / Separation of Sister Chromatids / microtubule cytoskeleton / microtubule binding / microtubule / cell division / centrosome / ATP hydrolysis activity / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
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 ...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: 2.15 Å
AuthorsWang, J. / Shen, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the kif2c motor domain
Authors: Wang, J. / Shen, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Structure summary / Category: software / struct / Item: _struct.title
Revision 1.4Aug 30, 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 / struct_ref_seq_dif / struct_site
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_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.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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KIF2C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,74713
Polymers43,2961
Non-polymers45212
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.720, 79.720, 154.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsnot known

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Components

#1: Protein KIF2C protein / Kinesin-like 6 / Mitotic centromere-associated kinesin / Kinesin family member 2C


Mass: 43295.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2C / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE-3)-RIL / References: UniProt: Q99661
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 291 K / pH: 7
Details: 37% PEG400, 0.2M NaCl, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 51791 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.9
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4 % / Rmerge(I) obs: 0.713

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.34 Å
Translation2.5 Å29.34 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
ARP/wARPmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V8K

1v8k


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.544 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1380 4.955 %RANDOM
Rwork0.22 ---
obs0.22126 27850 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.012 Å20 Å20 Å2
2---0.012 Å20 Å2
3---0.023 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 38 47 2578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222567
X-RAY DIFFRACTIONr_bond_other_d0.0020.021736
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9763472
X-RAY DIFFRACTIONr_angle_other_deg1.35934243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1295328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61323.627102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8715449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7161515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022822
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02523
X-RAY DIFFRACTIONr_nbd_refined0.1930.2459
X-RAY DIFFRACTIONr_nbd_other0.2060.21736
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21204
X-RAY DIFFRACTIONr_nbtor_other0.0790.21403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0210.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.85821697
X-RAY DIFFRACTIONr_mcbond_other0.4842661
X-RAY DIFFRACTIONr_mcangle_it4.08232600
X-RAY DIFFRACTIONr_scbond_it2.78321016
X-RAY DIFFRACTIONr_scangle_it3.9053868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 101 -
Rwork0.288 1891 -
obs--98.81 %

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