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- PDB-5jx1: The neck-linker and alpha 7 helix of Mus musculus KIF3A fused to EB1 -

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Basic information

Entry
Database: PDB / ID: 5jx1
TitleThe neck-linker and alpha 7 helix of Mus musculus KIF3A fused to EB1
ComponentsChimera protein of Kinesin-like protein KIF3A and Microtubule-associated protein RP/EB family member 1
KeywordsMOTOR PROTEIN / kinesin / coiled-coil
Function / homology
Function and homology information


epidermal stem cell homeostasis / kinesin II complex / intraciliary transport particle B binding / anterograde dendritic transport / Activation of SMO / Intraflagellar transport / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end ...epidermal stem cell homeostasis / kinesin II complex / intraciliary transport particle B binding / anterograde dendritic transport / Activation of SMO / Intraflagellar transport / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / centriole-centriole cohesion / anterograde dendritic transport of neurotransmitter receptor complex / positive regulation of keratinocyte proliferation / Kinesins / microtubule anchoring at centrosome / cilium movement / protein localization to microtubule / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / COPI-dependent Golgi-to-ER retrograde traffic / motile cilium assembly / Hedgehog 'off' state / microtubule plus-end / dorsal/ventral neural tube patterning / cell projection membrane / mitotic spindle microtubule / dentate gyrus development / attachment of mitotic spindle microtubules to kinetochore / MHC class II antigen presentation / microtubule bundle formation / microtubule plus-end binding / non-motile cilium assembly / dorsal/ventral pattern formation / protein localization to centrosome / determination of left/right symmetry / microtubule motor activity / anterior/posterior pattern specification / neural precursor cell proliferation / neural tube development / motile cilium / smoothened signaling pathway / spectrin binding / mitotic spindle pole / heart looping / spindle midzone / negative regulation of microtubule polymerization / forebrain development / microtubule polymerization / microtubule organizing center / establishment of mitotic spindle orientation / keratinocyte proliferation / cilium assembly / epidermis development / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / centriole / Recruitment of mitotic centrosome proteins and complexes / dendrite cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein serine/threonine kinase binding / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / positive regulation of epithelial cell proliferation / kidney development / RHO GTPases Activate Formins / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / intracellular protein localization / Regulation of PLK1 Activity at G2/M Transition / cell migration / heart development / microtubule binding / in utero embryonic development / microtubule / neuron projection / postsynapse / cilium / ciliary basal body / cadherin binding / cell division / focal adhesion / centrosome / glutamatergic synapse / Golgi apparatus / RNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Kinesin-like protein / Calponin homology (CH) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain ...EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Kinesin-like protein / Calponin homology (CH) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-like protein KIF3A / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsPhillips, R.K. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Family-specific Kinesin Structures Reveal Neck-linker Length Based on Initiation of the Coiled-coil.
Authors: Phillips, R.K. / Peter, L.G. / Gilbert, S.P. / Rayment, I.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimera protein of Kinesin-like protein KIF3A and Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)8,9231
Polymers8,9231
Non-polymers00
Water1,27971
1
A: Chimera protein of Kinesin-like protein KIF3A and Microtubule-associated protein RP/EB family member 1

A: Chimera protein of Kinesin-like protein KIF3A and Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)17,8462
Polymers17,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3970 Å2
ΔGint-32 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.812, 80.534, 36.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-105-

HOH

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Components

#1: Protein Chimera protein of Kinesin-like protein KIF3A and Microtubule-associated protein RP/EB family member 1 / Microtubule plus end-directed kinesin motor 3A / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 8923.008 Da / Num. of mol.: 1
Fragment: UNP P28741 residues 352-376,UNP Q15691 residues 210-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Kif3a, Kif3, MAPRE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28741, UniProt: Q15691
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.9 Å3/Da / Density % sol: 35.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24% (w/v) 2-methyl-2,4-pentanediol (MPD), 10% (w/v) PEG 4000, 100 mM CaCl2, 100 mM (3-(N-morpholino)propanesulfonic acid) (MOPS) pH 7.0, 1 mM CdCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.67→39.82 Å / Num. obs: 14745 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 50.1
Reflection shellResolution: 1.67→1.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 12.4 / % possible all: 86.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YIB

1yib


Resolution: 1.67→39.82 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 742 5.03 %
Rwork0.1923 --
obs0.194 14745 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms541 0 0 71 612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006573
X-RAY DIFFRACTIONf_angle_d0.716767
X-RAY DIFFRACTIONf_dihedral_angle_d22.231361
X-RAY DIFFRACTIONf_chiral_restr0.04284
X-RAY DIFFRACTIONf_plane_restr0.005101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6695-1.79840.20521440.19162476X-RAY DIFFRACTION86
1.7984-1.97940.27041440.20152816X-RAY DIFFRACTION96
1.9794-2.26580.22151490.17892896X-RAY DIFFRACTION99
2.2658-2.85460.25521530.19312913X-RAY DIFFRACTION100
2.8546-39.83140.20971520.19552902X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2967-0.5947-0.09792.7594-0.40140.23330.0366-0.0253-0.02210.3027-0.08860.11820.01920.03650.02220.05460.0033-0.02220.10690.00680.045920.681937.814812.4903
20.23760.5341-0.07654.029-2.36972.25090.09130.082-0.4319-0.2421-0.0291-0.0570.21690.25930.06290.08320.0331-0.00770.1218-0.00370.166630.204612.12854.7983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 73 )

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