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- PDB-7a5e: OSM-3 kinesin motor domain complexed with Mg.AMPPNP -

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Basic information

Entry
Database: PDB / ID: 7a5e
TitleOSM-3 kinesin motor domain complexed with Mg.AMPPNP
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 / cell projection organization ...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 / cell projection organization / non-motile cilium assembly / non-motile cilium / plus-end-directed microtubule motor activity / microtubule organizing center / kinesin complex / microtubule motor activity / cilium assembly / dendrite cytoplasm / ciliary basal body / cilium / microtubule binding / microtubule / neuron projection / dendrite / neuronal cell body / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Osmotic avoidance abnormal protein 3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 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 21, 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

Downloads & links

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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)78,53617
Polymers76,4462
Non-polymers2,09015
Water3,927218
1
A: Osmotic avoidance abnormal protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2228
Polymers38,2231
Non-polymers9997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Osmotic avoidance abnormal protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3149
Polymers38,2231
Non-polymers1,0918
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.03, 102.2, 140.95
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#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
Details: Alanine insertion at position 2 / Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: osm-3, M02B7.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P46873

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Non-polymers , 5 types, 233 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20% (W/V) polyethylene glycol 3350, 170 mM (NH4)2SO4, and 0.1 M Mes buffer 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: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 1.904→48.04 Å / Num. obs: 56649 / % possible obs: 99.8 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rrim(I) all: 0.098 / Net I/σ(I): 13.7
Reflection shellResolution: 1.904→1.95 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 8937 / CC1/2: 0.397

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A3Z

7a3z


Resolution: 1.904→48.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 2833 -RANDOM
Rwork0.2065 ---
obs0.2077 56649 99.8 %-
Displacement parametersBiso mean: 61.06 Å2
Baniso -1Baniso -2Baniso -3
1--12.3308 Å20 Å20 Å2
2--9.3915 Å20 Å2
3---2.9393 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.904→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5160 0 126 218 5504
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085398HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.957311HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1921SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes952HARMONIC5
X-RAY DIFFRACTIONt_it5398HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion723SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4266SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion15.6
LS refinement shellResolution: 1.904→1.92 Å
RfactorNum. reflection% reflection
Rfree0.4965 57 -
Rwork0.4198 --
obs--91.19 %
Refinement TLS params.

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)
11.19770.1951-0.17121.506-0.28622.92820.20030.5442-0.54420.54420.01010.2802-0.54420.2802-0.21040.1196-0.0461-0.0586-0.2227-0.0472-0.15873.3891-16.2737-1.7721
21.89880.12590.68851.7916-0.30052.808-0.0823-0.3192-0.0385-0.31920.17130.0978-0.03850.0978-0.089-0.0704-0.0814-0.0144-0.0230.0618-0.1531-16.4501-45.6448-33.2096
31.30370.1668-0.18052.6303-1.09582.87750.1530.521-0.42280.5210.1603-0.3032-0.4228-0.3032-0.3133-0.03110.07630.0611-0.10930.0251-0.0414-9.7092-18.6145-13.1936
41.710.17960.63441.8522-0.73732.24150.0193-0.19110.5442-0.19110.1365-0.00810.5442-0.0081-0.15590.0056-0.0465-0.0275-0.1115-0.0001-0.0894-16.9234-59.772-22.7883
51.09360.4603-0.03713.0908-0.70721.99390.10480.54420.02160.54420.1062-0.10720.0216-0.1072-0.2110.0358-0.0117-0.0184-0.12530.0359-0.0719-8.1333-32.1774-5.1854
63.07820.8210.45893.07870.14322.21090.0304-0.29790.3611-0.29790.2011-0.48370.3611-0.4837-0.2315-0.0634-0.152-0.0981-0.01640.0544-0.1255-31.0344-59.351-31.2228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|79 A|90 - A|126 A|295 - A|551 }
2X-RAY DIFFRACTION2{ B|1 - B|79 B|90 - B|126 B|295 - B|551 }
3X-RAY DIFFRACTION3{ A|80 - A|89 A|127 - A|155 A|171 - A|238 }
4X-RAY DIFFRACTION4{ B|80 - B|89 B|127 - B|155 B|171 - B|238 }
5X-RAY DIFFRACTION5{ A|156 - A|170 A|239 - A|294 }
6X-RAY DIFFRACTION6{ B|156 - B|170 B|239 - B|294 }

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