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

ID or keywords:

Entry

Database: PDB / ID: 8y9r

Title

Crystal structure of Spiral2 microtubule-binding domain from Physcomitrella patens

Components

Microtubule binding protein

Keywords

PLANT PROTEIN / structural protein

Function / homology

Function and homology information

microtubule binding / microtubule
Similarity search - Function

Biological species

Physcomitrium patens (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.799 Å

Authors

Hayashi, I.

Funding support

Japan, 1items

Citation

Journal: 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

Deposition	Feb 7, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8y9r.cif.gz	223.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8y9r.ent.gz	177.4 KB	Display	PDB format
PDBx/mmJSON format	8y9r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y9/8y9r ftp://data.pdbj.org/pub/pdb/validation_reports/y9/8y9r	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#85 - Jan 2007 Importins similarity (2)

Deposited unit

A: Microtubule binding protein

B: Microtubule binding protein

62.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Microtubule binding protein

defined by author
Evidence: gel filtration
31.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Microtubule binding protein

defined by author
31.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

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)

#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 interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.46 Å³/Da / Density % sol: 64.4 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97899 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 24, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97899 Å / Relative weight: 1
Reflection	Resolution: 2.7→48.11 Å / Num. obs: 24426 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC_1/2: 0.998 / R_merge(I) obs: 0.15 / R_pim(I) all: 0.063 / R_rim(I) all: 0.163 / Χ²: 0.99 / Net I/σ(I): 10 / Num. measured all: 161797
Reflection shell	Resolution: 2.7→2.83 Å / Redundancy: 6.5 % / R_merge(I) obs: 1.593 / Num. unique obs: 3148 / CC_1/2: 0.693 / R_pim(I) all: 0.673 / Χ²: 0.98

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
Aimless		data scaling
XDS		data reduction
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.799→48.095 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection
R_free	0.2764	1107	5.049 %
R_work	0.2149	20817	-
all	0.218	-	-
obs	-	21924	99.909 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 59.541 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.366 Å²	0 Å²	0 Å²
2-	-	4.995 Å²	-0 Å²
3-	-	-	-3.628 Å²

Refinement step

Cycle: LAST / Resolution: 2.799→48.095 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4222	0	0	25	4247

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	4275
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4331
X-RAY DIFFRACTION	r_angle_refined_deg	1.856	1.632	5794
X-RAY DIFFRACTION	r_angle_other_deg	0.623	1.566	9961
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.747	5	559
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	16.162	5	30
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.995	10	736
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.31	10	152
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	717
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4951
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	877
X-RAY DIFFRACTION	r_nbd_refined	0.25	0.2	1171
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.215	0.2	4205
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	2096
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2492
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.223	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.096	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.23	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.275	0.2	73
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.238	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	6.809	5.7	2248
X-RAY DIFFRACTION	r_mcbond_other	6.809	5.7	2248
X-RAY DIFFRACTION	r_mcangle_it	10.02	10.223	2803
X-RAY DIFFRACTION	r_mcangle_other	10.022	10.224	2804
X-RAY DIFFRACTION	r_scbond_it	7.148	6.405	2027
X-RAY DIFFRACTION	r_scbond_other	7.146	6.405	2027
X-RAY DIFFRACTION	r_scangle_it	10.762	11.515	2991
X-RAY DIFFRACTION	r_scangle_other	10.76	11.516	2992
X-RAY DIFFRACTION	r_lrange_it	13.867	58.173	4787
X-RAY DIFFRACTION	r_lrange_other	13.866	58.196	4788
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.105	0.05	8583

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10531	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10531	0.05009

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.799-2.872	0.435	82	0.374	1503	0.377	1589	0.834	0.868	99.7483	0.347
2.872-2.95	0.352	68	0.318	1482	0.319	1550	0.906	0.911	100	0.29
2.95-3.035	0.336	66	0.303	1440	0.305	1506	0.91	0.927	100	0.281
3.035-3.128	0.34	71	0.278	1403	0.281	1474	0.91	0.938	100	0.254
3.128-3.23	0.312	73	0.258	1331	0.261	1406	0.937	0.949	99.8577	0.235
3.23-3.343	0.311	81	0.23	1315	0.235	1396	0.944	0.963	100	0.203
3.343-3.469	0.304	70	0.224	1239	0.228	1309	0.944	0.968	100	0.205
3.469-3.61	0.233	62	0.205	1222	0.206	1285	0.971	0.974	99.9222	0.185
3.61-3.769	0.295	61	0.208	1192	0.212	1253	0.917	0.973	100	0.192
3.769-3.952	0.291	50	0.205	1118	0.209	1168	0.94	0.974	100	0.191
3.952-4.164	0.215	60	0.173	1080	0.175	1141	0.968	0.982	99.9124	0.163
4.164-4.415	0.258	62	0.164	993	0.169	1055	0.952	0.983	100	0.157
4.415-4.717	0.23	46	0.166	974	0.169	1021	0.971	0.984	99.9021	0.162
4.717-5.091	0.269	50	0.199	906	0.203	956	0.965	0.977	100	0.191
5.091-5.57	0.309	58	0.221	818	0.227	877	0.952	0.976	99.886	0.21
5.57-6.217	0.208	42	0.186	755	0.188	797	0.982	0.983	100	0.175
6.217-7.159	0.246	30	0.173	689	0.176	720	0.968	0.982	99.8611	0.171
7.159-8.72	0.198	28	0.143	594	0.145	623	0.98	0.988	99.8395	0.153
8.72-12.134	0.209	26	0.158	467	0.161	494	0.98	0.986	99.7976	0.179
12.134-48.095	0.407	21	0.402	296	0.403	318	0.877	0.892	99.6855	0.421

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