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- PDB-7a40: Nucleotide-free OSM-3 kinesin motor domain -

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Basic information

Entry
Database: PDB / ID: 7a40
TitleNucleotide-free OSM-3 kinesin motor domain
ComponentsOsmotic avoidance abnormal protein 3
KeywordsMOTOR PROTEIN / Kinesin-2 / Kif17 / motor domain / ATPase
Function / homology
Function and homology information


dauer entry / positive regulation of dauer larval development / negative regulation of non-motile cilium assembly / Intraflagellar transport / intraciliary anterograde transport / positive regulation of non-motile cilium assembly / intraciliary transport / regulation of insulin receptor signaling pathway / anterograde dendritic transport of neurotransmitter receptor complex / spindle elongation ...dauer entry / positive regulation of dauer larval development / negative regulation of non-motile cilium assembly / Intraflagellar transport / intraciliary anterograde transport / positive regulation of non-motile cilium assembly / intraciliary transport / regulation of insulin receptor signaling pathway / anterograde dendritic transport of neurotransmitter receptor complex / spindle elongation / cell projection organization / non-motile cilium assembly / non-motile cilium / plus-end-directed microtubule motor activity / microtubule organizing center / microtubule motor activity / kinesin complex / cilium assembly / dendrite cytoplasm / mitotic spindle organization / ciliary basal body / cilium / microtubule binding / microtubule / neuron projection / neuronal cell body / dendrite / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding
Similarity search - Function
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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Osmotic avoidance abnormal protein 3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å
AuthorsVarela, F.P. / Menetrey, J. / Gigant, B.
CitationJournal: Febs Open Bio / Year: 2021
Title: Structural snapshots of the kinesin-2 OSM-3 along its nucleotide cycle: implications for the ATP hydrolysis mechanism.
Authors: Varela, P.F. / Chenon, M. / Velours, C. / Verhey, K.J. / Menetrey, J. / Gigant, B.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: 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: Osmotic avoidance abnormal protein 3
B: Osmotic avoidance abnormal protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8236
Polymers76,4462
Non-polymers3764
Water1,17165
1
A: Osmotic avoidance abnormal protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4113
Polymers38,2231
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Osmotic avoidance abnormal protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4113
Polymers38,2231
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.770, 155.180, 63.720
Angle α, β, γ (deg.)90.000, 108.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Osmotic avoidance abnormal protein 3 / Kinesin-like protein osm-3


Mass: 38223.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: osm-3, M02B7.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P46873
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20% (W/V) polyethylene glycol 3350, 170 mM (NH4)2SO4, and 0.1 M Mes buffer at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.297→47.6 Å / Num. obs: 34809 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.997 / Rrim(I) all: 0.121 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6.6 % / Num. unique obs: 5500 / CC1/2: 0.625 / % possible all: 95.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A3Z

7a3z


Resolution: 2.297→47.59 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.261 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.213
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 1740 5 %RANDOM
Rwork0.2251 ---
obs0.2265 34801 99.6 %-
Displacement parametersBiso max: 169.59 Å2 / Biso mean: 86.85 Å2 / Biso min: 22.56 Å2
Baniso -1Baniso -2Baniso -3
1--4.1158 Å20 Å2-6.6888 Å2
2--11.7161 Å20 Å2
3----7.6003 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 2.297→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 22 65 4633
Biso mean--73.48 64.25 -
Num. residues----628
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1515SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes813HARMONIC5
X-RAY DIFFRACTIONt_it4644HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion659SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3579SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4644HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6319HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion18.08
LS refinement shellResolution: 2.3→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3377 34 4.88 %
Rwork0.2496 663 -
all0.2536 697 -
obs--85.12 %
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)
12.86370.6346-0.13457.82923.5966.451-0.16560.49750.6842-0.62360.10910.3265-0.46930.43960.0564-0.5359-0.00690.0784-0.5840.1317-0.36212.2206-22.93141.5997
24.033.1191-2.25767.8659-1.4723.0525-0.48270.6454-0.8896-0.70430.2685-0.78260.2114-0.34640.2142-0.4783-0.0620.2465-0.5908-0.156-0.14096.678-52.5665-30.3449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 338
2X-RAY DIFFRACTION2{ B|* }B1 - 337

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