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- PDB-2kin: KINESIN (MONOMERIC) FROM RATTUS NORVEGICUS -

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Basic information

Entry
Database: PDB / ID: 2kin
TitleKINESIN (MONOMERIC) FROM RATTUS NORVEGICUS
Components(KINESIN) x 2
KeywordsMOTOR PROTEIN / CYTOSKELETON
Function / homology
Function and homology information


response to rotenone / RHO GTPases activate KTN1 / Kinesins / distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / plus-end-directed kinesin ATPase / COPI-dependent Golgi-to-ER retrograde traffic / anterograde dendritic transport of neurotransmitter receptor complex / central region of growth cone / retrograde neuronal dense core vesicle transport ...response to rotenone / RHO GTPases activate KTN1 / Kinesins / distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / plus-end-directed kinesin ATPase / COPI-dependent Golgi-to-ER retrograde traffic / anterograde dendritic transport of neurotransmitter receptor complex / central region of growth cone / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / MHC class II antigen presentation / apolipoprotein receptor binding / intracellular mRNA localization / ciliary rootlet / apical dendrite / thalamus development / motor neuron axon guidance / plus-end-directed microtubule motor activity / kinesin complex / microtubule motor activity / synaptic vesicle transport / cellular response to ethanol / kinesin binding / mRNA transport / neuron development / postsynaptic cytosol / axonal growth cone / microtubule-based process / vesicle-mediated transport / axon cytoplasm / dendrite cytoplasm / axon guidance / hippocampus development / P-body / cellular response to nerve growth factor stimulus / cerebral cortex development / GABA-ergic synapse / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / scaffold protein binding / perikaryon / microtubule binding / microtubule / neuron projection / axon / neuronal cell body / dendrite / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #980 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1590 / 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. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #980 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1590 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Kinesin motor domain superfamily / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Special / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Kinesin heavy chain isoform 5C / Kinesin heavy chain isoform 5A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSack, S. / Muller, J. / Kozielski, F. / Marx, A. / Thormahlen, M. / Biou, V. / Mandelkow, E.-M. / Brady, S.T. / Mandelkow, E.
Citation
Journal: Biochemistry / Year: 1997
Title: X-ray structure of motor and neck domains from rat brain kinesin.
Authors: Sack, S. / Muller, J. / Marx, A. / Thormahlen, M. / Mandelkow, E.M. / Brady, S.T. / Mandelkow, E.
#1: Journal: J.Struct.Biol. / Year: 1997
Title: Crystallization and Preliminary X-Ray Analysis of the Single-Headed and Double-Headed Motor Protein Kinesin
Authors: Kozielski, F. / Schonbrunn, E. / Sack, S. / Muller, J. / Brady, S.T. / Mandelkow, E.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: The Crystal Structure of Dimeric Kinesin and Implications for Microtubule-Dependent Motility
Authors: Kozielski, F. / Sack, S. / Marx, A. / Thormahlen, M. / Schonbrunn, E. / Biou, V. / Thompson, A. / Mandelkow, E.M. / Mandelkow, E.
History
DepositionApr 28, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KINESIN
B: KINESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9586
Polymers38,2432
Non-polymers7154
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-74 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.556, 73.674, 74.128
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


Mass: 27072.869 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, MOTOR DOMAIN / Mutation: G293D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P56536*PLUS
#2: Protein KINESIN


Mass: 11169.800 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, MOTOR DOMAIN / Mutation: G293D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: Q6QLM7*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.46 Å3/Da / Density % sol: 49.6 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP METHOD WAS USED. PROTEIN WAS CRYSTALLIZED FROM 20MM PIPES, PH 7.5, 50MM KCL, 1MM EGTA, 1MM DTT, 0.9 M LI2SO4. THE RESERVOIR CONTAINED 1.8 M LITHIUM SULFATE IN THE SAME BUFFER., ...Details: HANGING DROP METHOD WAS USED. PROTEIN WAS CRYSTALLIZED FROM 20MM PIPES, PH 7.5, 50MM KCL, 1MM EGTA, 1MM DTT, 0.9 M LI2SO4. THE RESERVOIR CONTAINED 1.8 M LITHIUM SULFATE IN THE SAME BUFFER., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19-14 mg/mlprotein1drop
220 mMPIPES1drop
350 mM1dropKCl
41 mMEGTA1drop
51 mMdithiothreitol1drop
60.9 Mlithium sulfate1drop
71.8 Mlithium sulfate1reservoir
820 mMPIPES1reservoir
950 mM1reservoirKCl
101 mMEGTA1reservoir
111 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 28, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 32107 / % possible obs: 99.3 % / Redundancy: 5.1 % / Rsym value: 0.048 / Net I/σ(I): 13.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.2 % / Rsym value: 0.19 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 301422 / Rmerge(I) obs: 0.048

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNREFINED KINESIN DIMER

Resolution: 2→6 Å / Cross valid method: FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2663 10 %RANDOM
Rwork0.194 ---
obs-27128 --
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 27 205 2900
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_deg1.7

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