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- PDB-5jvr: The neck-linker of Mus musculus KIF3A fused to the alpha 7 helix ... -

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Basic information

Entry
Database: PDB / ID: 5jvr
TitleThe neck-linker of Mus musculus KIF3A fused to the alpha 7 helix of Drosophila melanogaster Kinesin-1 fused to EB1
ComponentsChimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
KeywordsMOTOR PROTEIN / kinesin / coiled-coil
Function / homology
Function and homology information


actin filament bundle organization / ovarian nurse cell to oocyte transport / anterograde axonal transport of mitochondrion / isoflavonoid biosynthetic process / mitochondrion distribution / regulation of pole plasm oskar mRNA localization / anterograde dendritic transport / eye photoreceptor cell differentiation / oocyte dorsal/ventral axis specification / larval locomotory behavior ...actin filament bundle organization / ovarian nurse cell to oocyte transport / anterograde axonal transport of mitochondrion / isoflavonoid biosynthetic process / mitochondrion distribution / regulation of pole plasm oskar mRNA localization / anterograde dendritic transport / eye photoreceptor cell differentiation / oocyte dorsal/ventral axis specification / larval locomotory behavior / pole plasm assembly / dorsal appendage formation / protein localization to astral microtubule / protein localization to mitotic spindle / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / oocyte microtubule cytoskeleton polarization / cortical microtubule cytoskeleton / pole plasm oskar mRNA localization / larval somatic muscle development / mitotic spindle astral microtubule end / centrosome separation / anterograde dendritic transport of neurotransmitter receptor complex / microtubule sliding / transport along microtubule / actin cap / protein localization to microtubule / cell projection membrane / microtubule plus-end / mitotic spindle microtubule / attachment of mitotic spindle microtubules to kinetochore / S-adenosylmethionine-dependent methyltransferase activity / microtubule plus-end binding / microtubule bundle formation / non-motile cilium assembly / O-methyltransferase activity / plus-end-directed microtubule motor activity / dendrite morphogenesis / protein localization to centrosome / axo-dendritic transport / microtubule motor activity / kinesin complex / microtubule-based movement / nuclear migration / stress granule disassembly / mitotic spindle pole / spindle midzone / establishment of mitotic spindle orientation / negative regulation of microtubule polymerization / intracellular distribution of mitochondria / tropomyosin binding / synaptic vesicle transport / microtubule polymerization / microtubule organizing center / cytoskeletal motor activity / regulation of microtubule polymerization or depolymerization / positive regulation of microtubule polymerization / cytoplasmic microtubule / spindle assembly / axonogenesis / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / dendrite cytoplasm / AURKA Activation by TPX2 / axon guidance / Resolution of Sister Chromatid Cohesion / protein serine/threonine kinase binding / RHO GTPases Activate Formins / intracellular protein localization / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / cell migration / methylation / microtubule binding / microtubule / protein dimerization activity / ciliary basal body / cadherin binding / cell division / focal adhesion / centrosome / Golgi apparatus / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / 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 / : / Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / 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 / : / Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Kinesin heavy chain / Coniferyl alcohol 9-O-methyltransferase / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Drosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 11, 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, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
B: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
C: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
D: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
E: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
F: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
G: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
H: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1


Theoretical massNumber of molelcules
Total (without water)71,9038
Polymers71,9038
Non-polymers00
Water7,224401
1
A: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
B: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1


Theoretical massNumber of molelcules
Total (without water)17,9762
Polymers17,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-34 kcal/mol
Surface area9230 Å2
MethodPISA
2
C: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
D: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1


Theoretical massNumber of molelcules
Total (without water)17,9762
Polymers17,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-34 kcal/mol
Surface area9940 Å2
MethodPISA
3
E: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
F: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1


Theoretical massNumber of molelcules
Total (without water)17,9762
Polymers17,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-33 kcal/mol
Surface area9970 Å2
MethodPISA
4
G: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1
H: Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1


Theoretical massNumber of molelcules
Total (without water)17,9762
Polymers17,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-31 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.172, 80.189, 155.375
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
Chimera protein of mouse KIF3A,fruit fly Kinesin-1 and human EB1 / Microtubule plus end-directed kinesin motor 3A / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 8987.933 Da / Num. of mol.: 8
Fragment: UNP P28741 residues 352-359,UNP P17210 residues 345-358,UNP Q15691 residues 207-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Homo sapiens (human)
Gene: Kif3a, Kif3, Khc, kin, CG7765, MAPRE1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P28741, UniProt: P17210, UniProt: Q15691
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 32% (w/v) polyethylene glycol dimethyl ether (DMPEG) 500, 30 mM MgCl2, 10 mM diethylenetriamine, 100 mM sodium 3-[4-(2-Hydroxyethyl)-1-piperazinyl]propanesulfonic acid (HEPPS) pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.1→43.88 Å / Num. obs: 52346 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 31.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 3.2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YIB

1yib


Resolution: 2.1→43.88 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 2607 4.98 %
Rwork0.196 --
obs0.198 52346 69.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 0 401 4801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014493
X-RAY DIFFRACTIONf_angle_d0.3286017
X-RAY DIFFRACTIONf_dihedral_angle_d19.9272786
X-RAY DIFFRACTIONf_chiral_restr0.032624
X-RAY DIFFRACTIONf_plane_restr0.002797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13820.30451000.25521911X-RAY DIFFRACTION51
2.1382-2.17930.26971020.23281927X-RAY DIFFRACTION52
2.1793-2.22380.26661030.23251956X-RAY DIFFRACTION52
2.2238-2.27220.25761010.22541933X-RAY DIFFRACTION52
2.2722-2.3250.24111030.23111938X-RAY DIFFRACTION52
2.325-2.38320.26711020.22821953X-RAY DIFFRACTION52
2.3832-2.44760.2891030.23171954X-RAY DIFFRACTION52
2.4476-2.51960.2991040.2381970X-RAY DIFFRACTION53
2.5196-2.60090.27241060.23422037X-RAY DIFFRACTION54
2.6009-2.69390.27541170.23722183X-RAY DIFFRACTION58
2.6939-2.80170.25351270.23172505X-RAY DIFFRACTION67
2.8017-2.92920.26651480.21352884X-RAY DIFFRACTION77
2.9292-3.08360.27191620.20663055X-RAY DIFFRACTION82
3.0836-3.27670.24631750.2033302X-RAY DIFFRACTION88
3.2767-3.52960.22241870.18813598X-RAY DIFFRACTION95
3.5296-3.88460.21821880.16633616X-RAY DIFFRACTION97
3.8846-4.44630.17881950.15123638X-RAY DIFFRACTION97
4.4463-5.60.21951960.16543684X-RAY DIFFRACTION99
5.6-43.88820.21571880.20463695X-RAY DIFFRACTION98
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)
11.7915-1.54430.05912.95731.09740.3681-0.03770.1949-0.33520.3303-0.03860.42620.21390.15140.07210.18660.00020.02210.2124-0.04740.182767.710.992312.3721
25.36120.64020.64085.16830.92574.88530.2156-0.08510.5411-0.851-0.0324-0.1315-0.4066-0.0529-0.01340.0699-0.02320.08720.17830.05160.127172.392626.937812.3055
30.55370.62420.50634.15010.55520.26770.10320.104-0.078-0.02190.0839-0.74660.18310.0837-0.34190.16740.02950.00660.2403-0.03240.199673.68143.644211.6383
46.7104-0.23910.34384.9233-0.94364.23680.3068-0.27980.45740.9441-0.15690.6499-0.01-0.5625-0.0270.1784-0.01410.0560.289-0.05620.234658.803224.434720.1906
51.9094-0.69910.50048.50980.09290.33660.1342-0.2096-0.16040.01160.05761.08260.1211-0.1302-0.0930.1385-0.0226-0.02290.30490.05570.187334.30513.707321.3755
65.7471-0.8124-1.61915.57242.33926.25970.4101-0.12370.7322-0.182-0.06450.2077-0.7020.2976-0.23510.1813-0.0550.07550.2220.01220.210248.244426.05916.9042
71.88820.90460.35113.9036-0.64710.71950.2403-0.0852-0.42910.16410.0398-0.56540.4866-0.0078-0.27050.28340.0476-0.05090.32120.04320.203740.72961.691819.9244
85.55320.28421.06723.476-1.84222.33560.3631-1.0420.77610.7638-0.13340.1931-0.5538-0.1305-0.08710.2408-0.00570.13040.3483-0.18230.291334.862826.790427.2761
91.7978-2.50771.99145.4643-3.52212.93670.1452-0.0224-0.3908-0.01730.09360.66630.136-0.1017-0.22830.1851-0.0393-0.03190.19420.01760.184353.4689-2.59389.2025
108.42551.35752.85968.05682.08988.01120.4432-0.2181-1.90170.6269-0.101-1.39391.09840.8723-0.20750.8084-0.0021-0.45910.76850.36531.245367.5205-34.053917.8364
115.07770.589-0.99962.2685-2.11872.37980.3178-0.0656-1.3023-0.0368-0.3086-1.29670.56370.19850.02680.47120.0947-0.14130.22-0.0240.632965.0777-26.83698.0831
125.2163-2.385-5.96591.1432.88327.4331-0.4983-0.34490.7131-1.09030.72130.17810.3790.76320.16910.59-0.14180.06240.42750.09550.515659.163225.4265-7.969
130.2738-1.2319-0.24393.9409-1.21060.42820.11860.148-0.1831-0.737-0.1487-0.26710.32170.00330.0130.3163-0.0165-0.08370.20070.00280.206256.1671-5.57633.534
143.7398-1.723-1.54194.73021.08626.0753-0.1276-0.3246-0.9520.0103-0.0760.02720.7024-0.0910.2560.3977-0.1228-0.12540.22680.14470.488250.5071-26.767717.9588
150.52041.4431-0.68933.0885-1.0210.79480.24030.1711-0.0179-0.0751-0.2798-0.0435-0.07810.28250.02730.4085-0.0223-0.06760.4147-0.10790.268165.40636.717443.9426
162.9051.1368-0.52164.9993-3.52693.6914-0.63160.3054-0.7931-0.2765-0.5565-1.11521.2707-0.17820.65660.89270.12410.02590.4946-0.20750.483765.771912.701836.8517
170.63271.2273-0.51357.07921.12111.0389-0.26370.32340.0605-1.38160.431-0.13970.2068-0.1047-0.12630.6396-0.0502-0.07220.6454-0.05170.217566.826736.644237.5166
188.00750.40970.0192.3544-1.18617.6171-0.17320.24560.08950.214-0.14240.86310.1754-0.71040.44790.3562-0.0068-0.1340.4809-0.09040.412354.146716.880949.3205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 10 THROUGH 46 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 47 THROUGH 74 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 7 THROUGH 48 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 49 THROUGH 71 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 8 THROUGH 48 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 49 THROUGH 74 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 7 THROUGH 48 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 49 THROUGH 75 )
9X-RAY DIFFRACTION9CHAIN 'E' AND (RESID 7 THROUGH 48 )
10X-RAY DIFFRACTION10CHAIN 'E' AND (RESID 49 THROUGH 54 )
11X-RAY DIFFRACTION11CHAIN 'E' AND (RESID 55 THROUGH 68 )
12X-RAY DIFFRACTION12CHAIN 'F' AND (RESID 1 THROUGH 8 )
13X-RAY DIFFRACTION13CHAIN 'F' AND (RESID 9 THROUGH 48 )
14X-RAY DIFFRACTION14CHAIN 'F' AND (RESID 49 THROUGH 75 )
15X-RAY DIFFRACTION15CHAIN 'G' AND (RESID 9 THROUGH 48 )
16X-RAY DIFFRACTION16CHAIN 'G' AND (RESID 49 THROUGH 71 )
17X-RAY DIFFRACTION17CHAIN 'H' AND (RESID 7 THROUGH 48 )
18X-RAY DIFFRACTION18CHAIN 'H' AND (RESID 49 THROUGH 69 )

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