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- PDB-8y9r: Crystal structure of Spiral2 microtubule-binding domain from Phys... -

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Basic information

Entry
Database: PDB / ID: 8y9r
TitleCrystal structure of Spiral2 microtubule-binding domain from Physcomitrella patens
ComponentsMicrotubule binding protein
KeywordsPLANT PROTEIN / structural protein
Function / homology
Function and homology information


microtubule binding / microtubule
Similarity search - Function
: / : / MT-associated protein TORTIFOLIA1/SPIRAL2-like / TORTIFOLIA1 C-terminal / TORTIFOLIA1 N-terminal / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
TOG domain-containing protein
Similarity search - Component
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.799 Å
AuthorsHayashi, I.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biochim Biophys Acta Mol Cell Res / Year: 2024
Title: Structural analysis of microtubule binding by minus-end targeting protein Spiral2.
Authors: Ohno, M. / Higuchi, Y. / Yamai, K. / Fuchigami, S. / Sasaki, T. / Oda, Y. / Hayashi, I.
History
DepositionFeb 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule binding protein
B: Microtubule binding protein


Theoretical massNumber of molelcules
Total (without water)62,1142
Polymers62,1142
Non-polymers00
Water45025
1
A: Microtubule binding protein


Theoretical massNumber of molelcules
Total (without water)31,0571
Polymers31,0571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microtubule binding protein


Theoretical massNumber of molelcules
Total (without water)31,0571
Polymers31,0571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.826, 95.646, 150.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ILE / End label comp-ID: ILE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 17 - 299 / Label seq-ID: 3 - 285

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Microtubule binding protein / TOG domain-containing protein


Mass: 31057.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_024812 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K1IUB4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.46 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate (pH 5.0), 0.2 M NaH2SO4, 50 mM guanidine hydrochloride and 1.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97899 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.7→48.11 Å / Num. obs: 24426 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.063 / Rrim(I) all: 0.163 / Χ2: 0.99 / Net I/σ(I): 10 / Num. measured all: 161797
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.593 / Num. unique obs: 3148 / CC1/2: 0.693 / Rpim(I) all: 0.673 / Χ2: 0.98

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.799→48.095 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.241 / SU ML: 0.298 / Cross valid method: FREE R-VALUE / ESU R: 0.645 / ESU R Free: 0.356
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2764 1107 5.049 %
Rwork0.2149 20817 -
all0.218 --
obs-21924 99.909 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.541 Å2
Baniso -1Baniso -2Baniso -3
1--1.366 Å20 Å20 Å2
2--4.995 Å2-0 Å2
3----3.628 Å2
Refinement stepCycle: LAST / Resolution: 2.799→48.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 0 25 4247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124275
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164331
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.6325794
X-RAY DIFFRACTIONr_angle_other_deg0.6231.5669961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7475559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.162530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99510736
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.3110152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02877
X-RAY DIFFRACTIONr_nbd_refined0.250.21171
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.24205
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22096
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22492
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0960.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.219
X-RAY DIFFRACTIONr_nbd_other0.2750.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2380.24
X-RAY DIFFRACTIONr_mcbond_it6.8095.72248
X-RAY DIFFRACTIONr_mcbond_other6.8095.72248
X-RAY DIFFRACTIONr_mcangle_it10.0210.2232803
X-RAY DIFFRACTIONr_mcangle_other10.02210.2242804
X-RAY DIFFRACTIONr_scbond_it7.1486.4052027
X-RAY DIFFRACTIONr_scbond_other7.1466.4052027
X-RAY DIFFRACTIONr_scangle_it10.76211.5152991
X-RAY DIFFRACTIONr_scangle_other10.7611.5162992
X-RAY DIFFRACTIONr_lrange_it13.86758.1734787
X-RAY DIFFRACTIONr_lrange_other13.86658.1964788
X-RAY DIFFRACTIONr_ncsr_local_group_10.1050.058583
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.105310.05009
12AX-RAY DIFFRACTIONLocal ncs0.105310.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.799-2.8720.435820.37415030.37715890.8340.86899.74830.347
2.872-2.950.352680.31814820.31915500.9060.9111000.29
2.95-3.0350.336660.30314400.30515060.910.9271000.281
3.035-3.1280.34710.27814030.28114740.910.9381000.254
3.128-3.230.312730.25813310.26114060.9370.94999.85770.235
3.23-3.3430.311810.2313150.23513960.9440.9631000.203
3.343-3.4690.304700.22412390.22813090.9440.9681000.205
3.469-3.610.233620.20512220.20612850.9710.97499.92220.185
3.61-3.7690.295610.20811920.21212530.9170.9731000.192
3.769-3.9520.291500.20511180.20911680.940.9741000.191
3.952-4.1640.215600.17310800.17511410.9680.98299.91240.163
4.164-4.4150.258620.1649930.16910550.9520.9831000.157
4.415-4.7170.23460.1669740.16910210.9710.98499.90210.162
4.717-5.0910.269500.1999060.2039560.9650.9771000.191
5.091-5.570.309580.2218180.2278770.9520.97699.8860.21
5.57-6.2170.208420.1867550.1887970.9820.9831000.175
6.217-7.1590.246300.1736890.1767200.9680.98299.86110.171
7.159-8.720.198280.1435940.1456230.980.98899.83950.153
8.72-12.1340.209260.1584670.1614940.980.98699.79760.179
12.134-48.0950.407210.4022960.4033180.8770.89299.68550.421

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