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- PDB-7kfl: Crystal structure of the cargo-binding domain from the plant clas... -

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Basic information

Entry
Database: PDB / ID: 7kfl
TitleCrystal structure of the cargo-binding domain from the plant class XI myosin (MyoXIk)
ComponentsMyosin-17
KeywordsMOTOR PROTEIN / class XI myosin / cargo-binding domain
Function / homology
Function and homology information


root hair cell tip growth / peroxisome localization / leaf pavement cell development / root hair tip / trichome morphogenesis / fruit development / trichome branching / gynoecium development / microfilament motor activity => GO:0000146 / unidimensional cell growth ...root hair cell tip growth / peroxisome localization / leaf pavement cell development / root hair tip / trichome morphogenesis / fruit development / trichome branching / gynoecium development / microfilament motor activity => GO:0000146 / unidimensional cell growth / root hair elongation / Golgi localization / mitochondrion localization / actin filament-based movement / plasmodesma / vesicle transport along actin filament / myosin complex / microfilament motor activity / cytoskeletal motor activity / transport vesicle / post-embryonic development / actin filament organization / actin filament binding / actin cytoskeleton / vesicle / calmodulin binding / cell division / ATP binding / cytoplasm
Similarity search - Function
Plant myosin, class XI, motor domain / Class XI myosin, cargo binding domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Myosin N-terminal SH3-like domain / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. ...Plant myosin, class XI, motor domain / Class XI myosin, cargo binding domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Myosin N-terminal SH3-like domain / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsTurowski, V.R. / Ruiz, D.M. / Nascimento, A.F.Z. / Millan, C. / Sammito, M.D. / Juanhuix, J. / Cremonesi, A.S. / Uson, I. / Giuseppe, P.O. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/09720-9 Brazil
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structure of the class XI myosin globular tail reveals evolutionary hallmarks for cargo recognition in plants.
Authors: Turowski, V.R. / Ruiz, D.M. / Nascimento, A.F.Z. / Millan, C. / Sammito, M.D. / Juanhuix, J. / Cremonesi, A.S. / Uson, I. / Giuseppe, P.O. / Murakami, M.T.
History
DepositionOct 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Myosin-17
B: Myosin-17


Theoretical massNumber of molelcules
Total (without water)89,3482
Polymers89,3482
Non-polymers00
Water1,11762
1
A: Myosin-17


Theoretical massNumber of molelcules
Total (without water)44,6741
Polymers44,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-17


Theoretical massNumber of molelcules
Total (without water)44,6741
Polymers44,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.062, 54.333, 113.432
Angle α, β, γ (deg.)90.000, 96.600, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Myosin-17 / / Myosin XI K / AtXIK


Mass: 44674.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: XI-K, XIK, At5g20490, F7C8.80 / Production host: Escherichia coli (E. coli) / References: UniProt: F4K5J1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 75 mM Bis-Tris pH 7.5, 0.2 M MgCl2, 25% (w/v) PEG 3350 and 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.35→47.36 Å / Num. obs: 37294 / % possible obs: 99.29 % / Redundancy: 3.2 % / Biso Wilson estimate: 53.42 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1264 / Net I/σ(I): 7.08
Reflection shellResolution: 2.35→2.434 Å / Rmerge(I) obs: 1.368 / Num. unique obs: 3671 / CC1/2: 0.456

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J5L

4j5l


Resolution: 2.35→47.36 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 30.388 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 1875 5 %RANDOM
Rwork0.2323 ---
obs0.2343 35418 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.91 Å2 / Biso mean: 66.004 Å2 / Biso min: 39.84 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å20.8 Å2
2--4.96 Å20 Å2
3----2.85 Å2
Refinement stepCycle: final / Resolution: 2.35→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5557 0 0 62 5619
Biso mean---55.24 -
Num. residues----692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135655
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175492
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.6317650
X-RAY DIFFRACTIONr_angle_other_deg1.0641.57812607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7065685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94422.767300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.841151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1711536
X-RAY DIFFRACTIONr_chiral_restr0.0390.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026333
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021327
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 130 -
Rwork0.426 2608 -
all-2738 -
obs--99.02 %
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)
10.7426-0.0156-0.62680.02550.15871.40680.02440.0086-0.0292-0.0170.0053-0.0021-0.136-0.0044-0.02960.04010.03030.00820.03980.00960.054863.247555.167339.6279
21.4187-0.46-0.65980.16590.32041.0922-0.04990.1319-0.12160.0131-0.03260.05760.01470.00390.08240.0046-0.0015-0.00830.0379-0.00160.104633.932149.9121.2481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1105 - 1499
2X-RAY DIFFRACTION2B1112 - 1499

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