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- PDB-3kin: KINESIN (DIMERIC) FROM RATTUS NORVEGICUS -

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Basic information

Entry
Database: PDB / ID: 3kin
TitleKINESIN (DIMERIC) FROM RATTUS NORVEGICUS
Components(KINESIN HEAVY CHAIN) 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 / COPI-dependent Golgi-to-ER retrograde traffic / plus-end-directed kinesin ATPase / 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 / COPI-dependent Golgi-to-ER retrograde traffic / plus-end-directed kinesin ATPase / anterograde dendritic transport of neurotransmitter receptor complex / central region of growth cone / retrograde neuronal dense core vesicle transport / MHC class II antigen presentation / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / thalamus development / apical dendrite / motor neuron axon guidance / cellular response to ethanol / plus-end-directed microtubule motor activity / kinesin complex / microtubule motor activity / ciliary rootlet / synaptic vesicle transport / kinesin binding / postsynaptic cytosol / mRNA transport / neuron development / microtubule-based process / axonal growth cone / vesicle-mediated transport / axon cytoplasm / dendrite cytoplasm / axon guidance / hippocampus development / GABA-ergic synapse / P-body / cellular response to nerve growth factor stimulus / cerebral cortex development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / microtubule binding / scaffold protein binding / perikaryon / 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 - #1980 / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1980 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 / MIRAS / Resolution: 3.1 Å
AuthorsKozielski, F. / Sack, S. / Marx, A. / Thormahlen, M. / Schonbrunn, E. / Biou, V. / Thompson, A. / Mandelkow, E.-M. / Mandelkow, E.
Citation
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.
#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: 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.
History
DepositionAug 25, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / 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

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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
C: KINESIN HEAVY CHAIN
D: KINESIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4976
Polymers80,6424
Non-polymers8542
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15980 Å2
ΔGint-112 kcal/mol
Surface area34420 Å2
MethodPISA
2
A: KINESIN HEAVY CHAIN
B: KINESIN HEAVY CHAIN
hetero molecules

C: KINESIN HEAVY CHAIN
D: KINESIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4976
Polymers80,6424
Non-polymers8542
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_464-x-1/2,-y+1,z-1/21
Buried area14680 Å2
ΔGint-100 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.150, 91.850, 141.680
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: 27072.869 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN
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 HEAVY CHAIN


Mass: 13248.242 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP METHOD WAS USED. PROTEIN WAS CRYSTALLIZED FROM 20MM PIPES, PH 7.5, 200MM NACL, 2MM DTT, 2 MM NA-EGTA, 0.8 M AS. THE RESERVOIR CONTAINED 1.6 M AS IN THE SAME BUFFER., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 mMPIPES1drop
32 mMdithiothreitol1drop
42 mMNa EGTA1drop
5200 mM1dropNaCl
60.8 Mammonium sulfate1drop
71.6 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 19516 / % possible obs: 100 % / Rsym value: 0.064 / Net I/σ(I): 10.7
Reflection
*PLUS
Num. measured all: 113071 / Rmerge(I) obs: 0.064

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Processing

Software
NameClassification
PHASESphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.1→6 Å / Cross valid method: FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.362 1491 10 %RANDOM
obs0.289 15124 --
Refinement stepCycle: LAST / Resolution: 3.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5629 0 54 60 5743

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