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- PDB-7wrg: Crystal structure of full-length kinesin-3 KLP-6 -

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Basic information

Entry
Database: PDB / ID: 7wrg
TitleCrystal structure of full-length kinesin-3 KLP-6
ComponentsKinesin-like protein
KeywordsTRANSPORT PROTEIN / Kinesin / ATPase
Function / homology
Function and homology information


COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / cytoskeleton-dependent intracellular transport / non-motile cilium / microtubule motor activity / kinesin complex / microtubule-based movement / mitochondrial membrane / microtubule binding / microtubule ...COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / cytoskeleton-dependent intracellular transport / non-motile cilium / microtubule motor activity / kinesin complex / microtubule-based movement / mitochondrial membrane / microtubule binding / microtubule / axon / neuronal cell body / dendrite / ATP hydrolysis activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Kinesin-like KIF1-type / Kinesin protein 1B / FHA domain / Forkhead-associated (FHA) 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 ...Kinesin-like KIF1-type / Kinesin protein 1B / FHA domain / Forkhead-associated (FHA) 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 / SMAD/FHA domain superfamily / Kinesin motor domain superfamily / C2 domain superfamily / S4 RNA-binding domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Kinesin-like protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsWang, W.J. / Ren, J.Q. / Song, W.Y. / Feng, W.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2022
Title: The architecture of kinesin-3 KLP-6 reveals a multilevel-lockdown mechanism for autoinhibition.
Authors: Wang, W. / Ren, J. / Song, W. / Zhang, Y. / Feng, W.
History
DepositionJan 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein
B: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,5546
Polymers214,6512
Non-polymers9034
Water543
1
A: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7773
Polymers107,3261
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-19 kcal/mol
Surface area38350 Å2
MethodPISA
2
B: Kinesin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7773
Polymers107,3261
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-18 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.138, 68.816, 253.216
Angle α, β, γ (deg.)90.000, 92.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kinesin-like protein


Mass: 107325.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: klp-6, CELE_R144.1, R144.1 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G5EFQ4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Sodium Malonate, 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.16→50 Å / Num. obs: 32692 / % possible obs: 98.9 % / Redundancy: 6.6 % / CC1/2: 0.95 / CC star: 0.987 / Net I/σ(I): 9.3
Reflection shellResolution: 3.16→3.31 Å / Mean I/σ(I) obs: 2.66 / Num. unique obs: 3292 / CC1/2: 0.811 / CC star: 0.946

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A1Z, 5B64, 3FM8

6a1z

5b64

3fm8


Resolution: 3.16→33.2 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2626 1622 4.97 %
Rwork0.2131 31021 -
obs0.2157 32643 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.35 Å2 / Biso min: 4.87 Å2
Refinement stepCycle: final / Resolution: 3.16→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12530 0 56 3 12589
Biso mean--69.34 19.92 -
Num. residues----1595
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.16-3.260.30631160.2775220785
3.26-3.360.34681410.2599260199
3.36-3.480.31181350.2496259399
3.48-3.620.2791320.2384259598
3.62-3.780.27061100.2325259998
3.78-3.980.29191180.2172265499
3.98-4.230.23711370.2067262999
4.23-4.560.25461470.18432587100
4.56-5.020.21291480.1812261699
5.02-5.740.24161380.2042261598
5.74-7.220.28591500.23172652100
7.22-100.23791500.1844267397

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