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- PDB-5hle: Structural basis of backwards motion in kinesin-14: minus-end dir... -

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Basic information

Entry
Database: PDB / ID: 5hle
TitleStructural basis of backwards motion in kinesin-14: minus-end directed nKn664 in the ADP state
ComponentsProtein claret segregational,Minus-end kinesin-1/kinesin-14,Protein claret segregational
KeywordsHYDROLASE / kinesin / kinesin-14 / microtubule / ATPase
Function / homology
Function and homology information


T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding
Similarity search - Function
Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / Kinesin motor domain / Kinesin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Capsid protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNitta, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: To Be Published
Title: Backwards motion in kinesin-14 requires neck-mimic to control a neck-helix swing.
Authors: Yamagishi, M. / Shigematsu, H. / Yokoyama, T. / Kikkawa, M. / Sugawa, M. / Aoki, M. / Shirouzu, M. / Yajima, J. / Nitta, R.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein claret segregational,Minus-end kinesin-1/kinesin-14,Protein claret segregational
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0723
Polymers41,6201
Non-polymers4522
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-17 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.858, 112.858, 72.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein claret segregational,Minus-end kinesin-1/kinesin-14,Protein claret segregational


Mass: 41620.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Rattus norvegicus (Norway rat)
Production host: Escherichia coli (E. coli) / References: UniProt: P20480
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, Ammonium sulfate, HEPES Benzamidine-HCl, ADP

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 12353 / % possible obs: 100 % / Redundancy: 5.7 % / Net I/σ(I): 18.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BG2

1bg2


Resolution: 2.9→19.548 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.09
RfactorNum. reflection% reflection
Rfree0.2872 1171 10.04 %
Rwork0.2109 --
obs0.2185 11668 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 28 3 2400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112437
X-RAY DIFFRACTIONf_angle_d1.5733293
X-RAY DIFFRACTIONf_dihedral_angle_d18.766914
X-RAY DIFFRACTIONf_chiral_restr0.057375
X-RAY DIFFRACTIONf_plane_restr0.006421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9004-3.0320.36621440.28451282X-RAY DIFFRACTION100
3.032-3.19120.36451440.26761320X-RAY DIFFRACTION100
3.1912-3.39010.32311440.2431302X-RAY DIFFRACTION100
3.3901-3.65030.30381510.21381313X-RAY DIFFRACTION100
3.6503-4.01480.2751430.20041307X-RAY DIFFRACTION100
4.0148-4.58920.27851440.17781309X-RAY DIFFRACTION100
4.5892-5.75730.25131480.20091323X-RAY DIFFRACTION100
5.7573-19.5480.26221530.20051341X-RAY DIFFRACTION100

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