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- PDB-3kar: THE MOTOR DOMAIN OF KINESIN-LIKE PROTEIN KAR3, A SACCHAROMYCES CE... -

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Basic information

Entry
Database: PDB / ID: 3kar
TitleTHE MOTOR DOMAIN OF KINESIN-LIKE PROTEIN KAR3, A SACCHAROMYCES CEREVISIAE KINESIN-RELATED PROTEIN
ComponentsKINESIN-LIKE PROTEIN KAR3
KeywordsCONTRACTILE PROTEIN / KAR3 / KINESIN-RELATED PROTEIN / MOTOR PROTEIN / ATPASE / P-LOOP / MICROTUBULE BINDING PROTEIN
Function / homology
Function and homology information


minus-end-directed kinesin ATPase / nuclear migration involved in conjugation with cellular fusion / protein transport along microtubule to mitotic spindle pole body / karyogamy involved in conjugation with cellular fusion / mitotic spindle midzone assembly / spindle pole body / minus-end-directed microtubule motor activity / mitotic sister chromatid cohesion / microtubule-based process / cytoplasmic microtubule ...minus-end-directed kinesin ATPase / nuclear migration involved in conjugation with cellular fusion / protein transport along microtubule to mitotic spindle pole body / karyogamy involved in conjugation with cellular fusion / mitotic spindle midzone assembly / spindle pole body / minus-end-directed microtubule motor activity / mitotic sister chromatid cohesion / microtubule-based process / cytoplasmic microtubule / ERAD pathway / regulation of mitotic spindle organization / meiotic cell cycle / spindle pole / mitotic cell cycle / chromosome / microtubule cytoskeleton / 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 / MIR / Resolution: 2.3 Å
AuthorsGulick, A.M. / Song, H. / Endow, S. / Rayment, I.
CitationJournal: Biochemistry / Year: 1998
Title: X-ray crystal structure of the yeast Kar3 motor domain complexed with Mg.ADP to 2.3 A resolution.
Authors: Gulick, A.M. / Song, H. / Endow, S.A. / Rayment, I.
History
DepositionNov 26, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _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.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.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

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Assembly

Deposited unit
A: KINESIN-LIKE PROTEIN KAR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2583
Polymers38,8071
Non-polymers4522
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.129, 81.209, 48.298
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein KINESIN-LIKE PROTEIN KAR3


Mass: 38806.539 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 383 - 722 / Mutation: L383M
Source method: isolated from a genetically manipulated source
Details: GENETICALLY TRUNCATED MOTOR DOMAIN OF SACCHAROMYCES CEREVISIAE MOTOR PROTEIN KAR3 LIGANDS MG2 AND ADP
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: KAR3 / Plasmid: PMW-KAR3 / 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


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


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.14 Å3/Da / Density % sol: 42 %
Crystal growpH: 7
Details: 11 % MEPEG 2000, 50 MM NACL, 1% ETHYLENE GLYCOL, 1 MM MG ADP, pH 7.
Crystal grow
*PLUS
pH: 7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMprotein11
222 %methyl ether PEG200011
3100 mM11NaCl
42 %ethylene glycol11
550 mMHEPES11

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Data collection

DiffractionMean temperature: 269 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Apr 9, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 22220 / % possible obs: 93 % / Redundancy: 2 % / Rmerge(I) obs: 0.034
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.074 / % possible all: 85
Reflection
*PLUS
Num. measured all: 43898
Reflection shell
*PLUS
% possible obs: 84.7 %

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Processing

Software
NameClassification
HEAVYmodel building
TNTrefinement
XDSdata reduction
XSCALIBREdata scaling
HEAVYphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→30 Å
RfactorNum. reflection% reflection
Rwork0.175 --
obs-43898 93.2 %
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 28 105 2608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.15
X-RAY DIFFRACTIONt_dihedral_angle_d19.65
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006
X-RAY DIFFRACTIONt_gen_planes0.015
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.096
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.65
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.015

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