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- PDB-5jvs: The neck-linker + DAL and alpha 7 helix of Drosophila melanogaste... -

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Basic information

Entry
Database: PDB / ID: 5jvs
TitleThe neck-linker + DAL 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


actin filament bundle organization / ovarian nurse cell to oocyte transport / anterograde dendritic transport / anterograde axonal transport of mitochondrion / mitochondrion distribution / oocyte microtubule cytoskeleton polarization / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification ...actin filament bundle organization / ovarian nurse cell to oocyte transport / anterograde dendritic transport / anterograde axonal transport of mitochondrion / mitochondrion distribution / oocyte microtubule cytoskeleton polarization / eye photoreceptor cell differentiation / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / oocyte dorsal/ventral axis specification / larval locomotory behavior / pole plasm assembly / protein localization to astral microtubule / dorsal appendage formation / protein localization to mitotic spindle / cortical microtubule cytoskeleton / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / larval somatic muscle development / mitotic spindle astral microtubule end / centrosome separation / anterograde dendritic transport of neurotransmitter receptor complex / transport along microtubule / microtubule sliding / actin cap / protein localization to microtubule / microtubule plus-end / mitotic spindle microtubule / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule bundle formation / non-motile cilium assembly / microtubule plus-end binding / plus-end-directed microtubule motor activity / axo-dendritic transport / protein localization to centrosome / kinesin complex / microtubule motor activity / microtubule-based movement / stress granule disassembly / nuclear migration / negative regulation of microtubule polymerization / synaptic vesicle transport / dendrite morphogenesis / mitotic spindle pole / tropomyosin binding / spindle midzone / intracellular distribution of mitochondria / microtubule organizing center / microtubule polymerization / cytoskeletal motor activity / establishment of mitotic spindle orientation / regulation of microtubule polymerization or depolymerization / spindle assembly / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / axon cytoplasm / 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 / dendrite cytoplasm / axonogenesis / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein serine/threonine kinase binding / axon guidance / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / RHO GTPases Activate Formins / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / cell migration / microtubule binding / microtubule / 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
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 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: 2.248 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, 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 heavy chain and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5003
Polymers10,3731
Non-polymers1272
Water48627
1
A: Chimera protein of Kinesin heavy chain and Microtubule-associated protein RP/EB family member 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)21,0006
Polymers20,7452
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-x,-y-1,z1
Buried area3750 Å2
ΔGint-33 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.016, 40.016, 185.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-32-

ASN

21A-101-

ZN

31A-209-

HOH

41A-212-

HOH

51A-220-

HOH

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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: 10372.621 Da / Num. of mol.: 1
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.78 Å3/Da / Density % sol: 31.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM sodium acetate pH 5.0, 24% (w/v) polyethylene glycol (PEG) 400, 80 mM MgCl2, 3 mM ZnSO4

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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: 2.24→46.34 Å / Num. obs: 5804 / % possible obs: 90 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 37.5
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 4.6 / % possible all: 69.5

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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: 2.248→33.588 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 287 4.94 %
Rwork0.2 --
obs0.202 5804 84.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.248→33.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms557 0 5 27 589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002576
X-RAY DIFFRACTIONf_angle_d0.33768
X-RAY DIFFRACTIONf_dihedral_angle_d10.178361
X-RAY DIFFRACTIONf_chiral_restr0.02877
X-RAY DIFFRACTIONf_plane_restr0.001103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2484-2.83250.31361140.24412267X-RAY DIFFRACTION70
2.8325-33.59140.21571730.18663250X-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)
10.6571-0.2179-0.40971.677-0.19884.5388-0.1667-0.0401-0.04780.53990.02780.13730.2420.27240.08460.09170.03640.01650.57520.07590.29112.1396-21.6948-2.9137
25.49-1.7562-1.32874.96682.92711.74240.09761.23240.7071-1.01130.1143-0.6406-0.64490.4464-0.24630.3442-0.13660.0060.7710.11730.3338-1.3922-13.8223-36.2288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 79 )

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