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- PDB-2y5w: Crystal structure of Drosophila melanogaster kinesin-1 motor doma... -

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Basic information

Entry
Database: PDB / ID: 2y5w
TitleCrystal structure of Drosophila melanogaster kinesin-1 motor domain dimer
ComponentsKINESIN HEAVY CHAIN
KeywordsMOTOR PROTEIN / MICROTUBULE ASSOCIATED / ATPASE
Function / homology
Function and homology information


actin filament bundle organization / ovarian nurse cell to oocyte transport / anterograde axonal transport of mitochondrion / anterograde dendritic transport / mitochondrion distribution / oocyte microtubule cytoskeleton polarization / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification ...actin filament bundle organization / ovarian nurse cell to oocyte transport / anterograde axonal transport of mitochondrion / anterograde dendritic transport / mitochondrion distribution / oocyte microtubule cytoskeleton polarization / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification / larval locomotory behavior / pole plasm assembly / dorsal appendage formation / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / larval somatic muscle development / centrosome separation / transport along microtubule / anterograde dendritic transport of neurotransmitter receptor complex / microtubule sliding / actin cap / microtubule plus-end / plus-end-directed microtubule motor activity / axo-dendritic transport / kinesin complex / microtubule motor activity / microtubule-based movement / nuclear migration / stress granule disassembly / dendrite morphogenesis / tropomyosin binding / synaptic vesicle transport / intracellular distribution of mitochondria / microtubule polymerization / cytoskeletal motor activity / axon cytoplasm / dendrite cytoplasm / axonogenesis / axon guidance / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
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 heavy chain
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKaan, H.Y.K. / Hackney, D.D. / Kozielski, F.
CitationJournal: Science / Year: 2011
Title: The Structure of the Kinesin-1 Motor-Tail Complex Reveals the Mechanism of Autoinhibition.
Authors: Kaan, H.Y.K. / Hackney, D.D. / Kozielski, F.
History
DepositionJan 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Structure summary
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KINESIN HEAVY CHAIN
B: KINESIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6746
Polymers81,7712
Non-polymers9034
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-15.9 kcal/mol
Surface area36930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.890, 89.180, 138.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KINESIN HEAVY CHAIN


Mass: 40885.301 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN, RESIDUES 1-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS / References: UniProt: P17210
#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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.82 Å3/Da / Density % sol: 56.44 % / Description: NONE
Crystal growpH: 7.8
Details: 24 % POLYETHYLENE GLYCOL-3350, 0.15 M AMMONIUM SULFATE, AND 0.1 M HEPES SODIUM PH 7.8

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 35890 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 55.874 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BG2

1bg2


Resolution: 2.7→29.74 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.859 / SU B: 12.502 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.664 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28883 1347 5 %RANDOM
Rwork0.20982 ---
obs0.21384 25608 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.125 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å20 Å2
2---2.72 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 56 180 5366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225297
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9637184
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5315672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94225.042240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.85715919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3431526
X-RAY DIFFRACTIONr_chiral_restr0.1270.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023951
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9291.53314
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78625355
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28231983
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9654.51823
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.695→2.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 85 -
Rwork0.273 1848 -
obs--100 %

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