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- PDB-1f9t: CRYSTAL STRUCTURES OF KINESIN MUTANTS REVEAL A SIGNALLING PATHWAY... -

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Basic information

Entry
Database: PDB / ID: 1f9t
TitleCRYSTAL STRUCTURES OF KINESIN MUTANTS REVEAL A SIGNALLING PATHWAY FOR ACTIVATION OF THE MOTOR ATPASE
ComponentsKINESIN-LIKE PROTEIN KAR3
KeywordsCONTRACTILE PROTEIN / Kar3 / Kinesin-related protein / motor protein / microtubule binding protein
Function / homology
Function and homology information


minus-end-directed kinesin ATPase / microtubule bundle formation involved in mitotic spindle midzone assembly / nuclear migration involved in conjugation with cellular fusion / protein transport along microtubule to mitotic spindle pole body / karyogamy involved in conjugation with cellular fusion / minus-end-directed microtubule motor activity / spindle pole body / mitotic sister chromatid cohesion / cytoplasmic microtubule / regulation of mitotic spindle organization ...minus-end-directed kinesin ATPase / microtubule bundle formation involved in mitotic spindle midzone assembly / nuclear migration involved in conjugation with cellular fusion / protein transport along microtubule to mitotic spindle pole body / karyogamy involved in conjugation with cellular fusion / minus-end-directed microtubule motor activity / spindle pole body / mitotic sister chromatid cohesion / cytoplasmic microtubule / regulation of mitotic spindle organization / isomerase activity / meiotic cell cycle / spindle pole / mitotic cell cycle / chromosome / microtubule binding / microtubule / cell division / ATP hydrolysis activity / ATP binding / nucleus
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 KAR3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsYun, M. / Zhang, X. / Park, C.-G. / Park, H.-W. / Endow, S.A.
CitationJournal: EMBO J. / Year: 2001
Title: A structural pathway for activation of the kinesin motor ATPase.
Authors: Yun, M. / Zhang, X. / Park, C.G. / Park, H.W. / Endow, S.A.
History
DepositionJul 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KINESIN-LIKE PROTEIN KAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8093
Polymers40,3571
Non-polymers4522
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.61, 78.81, 47.17
Angle α, β, γ (deg.)90.0, 105.01, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein KINESIN-LIKE PROTEIN KAR3


Mass: 40357.293 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN / Mutation: V372M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PMW174 / Production host: Escherichia coli (E. coli) / References: UniProt: P17119
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, PEG 2000 ME, magnesium chloride, Ethylen glycol, Sodium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / PH range low: 8 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220-26 %PEG2000 ME1reservoir
30.2 M1reservoirNaCl
450 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795
DetectorDetector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 47889 / Num. obs: 47889 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 16.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2 % / Num. unique all: 2343 / % possible all: 94.9
Reflection
*PLUS
Num. measured all: 793427
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.5→20 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.244 4196 -RANDOM
Rwork0.213 ---
all-43798 --
obs-41892 89 %-
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 28 289 2710
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.199
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS

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