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- PDB-5jvu: The neck-linker and alpha 7 helix of Drosophila melanogaster kine... -

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Basic information

Entry
Database: PDB / ID: 5jvu
TitleThe neck-linker and alpha 7 helix of Drosophila melanogaster kinesin-1 fused to EB1
ComponentsChimera protein of Kinesin heavy chain and Microtubule-associated protein RP/EB family member 1
KeywordsMOTOR PROTEIN / kinesin / coiled-coil
Function / homology
Function and homology information


anterograde axonal transport of mitochondrion / actin filament bundle organization / ovarian nurse cell to oocyte transport / anterograde dendritic transport / mitochondrion distribution / oocyte microtubule cytoskeleton polarization / larval locomotory behavior / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization ...anterograde axonal transport of mitochondrion / actin filament bundle organization / ovarian nurse cell to oocyte transport / anterograde dendritic transport / mitochondrion distribution / oocyte microtubule cytoskeleton polarization / larval locomotory behavior / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification / pole plasm assembly / protein localization to mitotic spindle / protein localization to astral microtubule / microtubule sliding / dorsal appendage formation / cortical microtubule cytoskeleton / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / larval somatic muscle development / mitotic spindle astral microtubule end / transport along microtubule / centrosome separation / anterograde dendritic transport of neurotransmitter receptor complex / actin cap / protein localization to microtubule / mitotic spindle microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / axo-dendritic transport / plus-end-directed microtubule motor activity / nuclear migration / stress granule disassembly / protein localization to centrosome / microtubule organizing center / dendrite morphogenesis / microtubule motor activity / kinesin complex / negative regulation of microtubule polymerization / synaptic vesicle transport / tropomyosin binding / microtubule-based movement / intracellular distribution of mitochondria / mitotic spindle pole / cytoplasmic microtubule / establishment of mitotic spindle orientation / microtubule polymerization / cytoskeletal motor activity / spindle midzone / spindle assembly / regulation of microtubule polymerization or depolymerization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / axon cytoplasm / Recruitment of NuMA to mitotic centrosomes / positive regulation of microtubule polymerization / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / dendrite cytoplasm / AURKA Activation by TPX2 / axonogenesis / ciliary basal body / axon guidance / RHO GTPases Activate Formins / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / protein localization / cell migration / microtubule binding / microtubule / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / cytosol / cytoplasm
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 profile. ...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 profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / 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 heavy chain / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å
AuthorsPhillips, R.K. / Rayment, I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37-GM54141 United States
National Science Foundation (NSF, United States)DGE-0718123 United States
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_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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

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Assembly

Deposited unit
A: Chimera protein of Kinesin heavy chain and Microtubule-associated protein RP/EB family member 1
B: Chimera protein of Kinesin heavy chain and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2093
Polymers20,1472
Non-polymers621
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-32 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.973, 37.783, 52.706
Angle α, β, γ (deg.)90.00, 114.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chimera protein of Kinesin heavy chain and Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 10073.299 Da / Num. of mol.: 2
Fragment: UNP P17210 residues 334-365,UNP Q15691 residues 207-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Homo sapiens (human)
Gene: Khc, kin, CG7765, MAPRE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17210, UniProt: Q15691
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% (w/v) methoxy polyethylene glycol (MEPEG) 5000, 100 mM Li2SO4, 100 mM MES/Acetate pH 5.5, 10 mM gamma-caprolactone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.948→28.263 Å / Num. obs: 12095 / % possible obs: 99 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.6
Reflection shellResolution: 1.948→2.072 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.1 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YIB

1yib


Resolution: 1.948→28.263 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 603 4.99 %
Rwork0.1979 --
obs0.2001 12095 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.948→28.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 4 155 1391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071265
X-RAY DIFFRACTIONf_angle_d0.7931693
X-RAY DIFFRACTIONf_dihedral_angle_d24.209795
X-RAY DIFFRACTIONf_chiral_restr0.043175
X-RAY DIFFRACTIONf_plane_restr0.005226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.948-2.1440.281410.22342591X-RAY DIFFRACTION89
2.144-2.4540.24971520.20052939X-RAY DIFFRACTION100
2.454-3.09120.26411550.19932952X-RAY DIFFRACTION100
3.0912-28.26560.21871550.18953010X-RAY DIFFRACTION99
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)
14.62720.1319-3.01270.57110.69691.3344-0.359-0.71580.00270.03730.1985-0.03650.25650.31150.18990.1720.031-0.04810.14930.09870.1262.90145.69416.2899
22.90410.2866-0.4213.7272-0.97144.9181-0.2578-0.0363-0.1771-0.0716-0.03820.60281.057-0.80010.09110.1702-0.11770.01610.1947-0.06740.2307-28.032646.018424.4742
37.503-0.9827-5.22450.73531.1373.6832-0.16170.28710.10960.05190.1811-0.13430.2359-0.2390.00350.12780.0129-0.07550.09950.02620.11470.503247.238213.4989
46.2020.15111.79186.84370.69752.5097-0.2041-1.5019-0.21261.5881-0.1510.78250.71640.30890.09280.5570.1050.07980.29260.04440.1776-20.724847.175939.4478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 86 )
3X-RAY DIFFRACTION3chain 'B' and (resid 10 through 60 )
4X-RAY DIFFRACTION4chain 'B' and (resid 61 through 78 )

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