PDB-9gnu: Tubulin in complex with a dioxane analog of zampanolide

ID or keywords:

Entry

Database: PDB / ID: 9gnu

Title

Tubulin in complex with a dioxane analog of zampanolide

Components

Stathmin-4
Tubulin alpha-1B chain
Tubulin beta-2B chain
Tubulin tyrosine ligase

Keywords

CELL CYCLE / tubulin / zampanolide / microtubule stabilizing agent

Function / homology

Function and homology information

tubulin-tyrosine ligase / regulation of metaphase plate congression / tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Gallus gallus (chicken)

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Oliva, M.A. / Diaz, J.F. / Altmann, K.H.

Funding support

Spain, 3items

Organization	Grant number	Country
Ministerio de Ciencia e Innovacion (MCIN)	CNS2023-145079	Spain
Ministerio de Ciencia e Innovacion (MCIN)	PID2021-123399OB-I00	Spain
Ministerio de Ciencia e Innovacion (MCIN)	PID2022-136765OB-I00	Spain

Citation

Journal: To Be Published
Title: Tubulin in complex with a dioxane analog of zampanolide
Authors: Oliva, M.A. / Diaz, J.F. / Altmann, K.H.

History

Deposition	Sep 4, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gnu.cif.gz	2 MB	Display	PDBx/mmCIF format
PDB format	pdb9gnu.ent.gz		Display	PDB format
PDBx/mmJSON format	9gnu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gnu_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	9gnu_full_validation.pdf.gz	2.2 MB	Display
Data in XML	9gnu_validation.xml.gz	72.9 KB	Display
Data in CIF	9gnu_validation.cif.gz	95.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gn/9gnu ftp://data.pdbj.org/pub/pdb/validation_reports/gn/9gnu	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	#175 - Jul 2014 Microtubules similarity (28) #176 - Aug 2014 Dynein similarity (19) #241 - Jan 2020 Twenty Years of Molecules similarity (19) #118 - Oct 2009 Sodium-Potassium Pump similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: Tubulin alpha-1B chain

B: Tubulin beta-2B chain

C: Tubulin alpha-1B chain

D: Tubulin beta-2B chain

E: Stathmin-4

F: Tubulin tyrosine ligase

hetero molecules

271 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	105.197, 159.166, 178.367
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A

NCS domain segments:

Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 438 / Label seq-ID: 2 - 438

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein	Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P81947
#2: Protein	Tubulin beta-2B chain Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856
#3: Protein	Stathmin-4 / Stathmin-like protein B3 / RB3 Mass: 22125.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#4: Protein	Tubulin tyrosine ligase Mass: 44378.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8V0Z8P0

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Non-polymers , 10 types, 901 molecules

#5: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Comment: GTP, energy-carrying molecule*YM
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#10: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#11: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#12: Chemical	ChemComp-A1IND / (2Z,4E)-N-((S)-((1R,2E,5S,8E,10Z,14E,17S)-3,11-dimethyl-7,13-dioxo-6,19,21-trioxabicyclo[15.3.1]henicosa-2,8,10,14-tetraen-5-yl)(hydroxy)methyl)hexa-2,4-dienamide / (2~{Z},4~{E})-~{N}-[(~{S})-[(1~{R},2~{E},5~{S},8~{E},10~{Z},17~{S})-3,11-dimethyl-7,13-bis(oxidanylidene)-6,19,21-trioxabicyclo[15.3.1]henicosa-2,8,10,14-tetraen-5-yl]-oxidanyl-methyl]hexa-2,4-dienamide Mass: 485.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₅NO₇ / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical	ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#14: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.8 Å³/Da / Density % sol: 56.03 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion Details: 0.1 M Mes / 0.1 M Imidazole pH 6.5, 0.03 M CaCl2 / 0.03 M MgCl2, 5 mM L-Tyrosine, 8 % glycerol, 5.5 % PEG4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 2.2→48.14 Å / Num. obs: 151850 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.081 / R_pim(I) all: 0.027 / R_rim(I) all: 0.086 / Net I/σ(I): 16.6
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 9.6 % / R_merge(I) obs: 1.163 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7406 / CC_1/2: 0.699 / R_pim(I) all: 0.391 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→48.139 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.947 / SU B: 10.301 / SU ML: 0.128 / Cross valid method: FREE R-VALUE / ESU R: 0.189 / ESU R Free: 0.165
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.2061	7610	5.015 %
R_work	0.1639	144149	-
all	0.166	-	-
obs	-	151759	99.853 %

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: 52.554 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.639 Å²	-0 Å²	0 Å²
2-	-	-0.79 Å²	-0 Å²
3-	-	-	-0.849 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→48.139 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17040	0	265	880	18185

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	18047
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	16606
X-RAY DIFFRACTION	r_angle_refined_deg	2.344	1.837	24540
X-RAY DIFFRACTION	r_angle_other_deg	0.868	1.759	38328
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.988	5	2217
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.649	5	137
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	12.085	5	29
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.233	10	3033
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.397	10	865
X-RAY DIFFRACTION	r_chiral_restr	0.114	0.2	2682
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	21453
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4202
X-RAY DIFFRACTION	r_nbd_refined	0.238	0.2	3692
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	15469
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	8814
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	10124
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.196	0.2	872
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.06	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.186	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.179	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.208	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	3.281	2.535	8802
X-RAY DIFFRACTION	r_mcbond_other	3.281	2.535	8802
X-RAY DIFFRACTION	r_mcangle_it	4.41	4.536	11053
X-RAY DIFFRACTION	r_mcangle_other	4.411	4.533	11042
X-RAY DIFFRACTION	r_scbond_it	5.397	3.102	9245
X-RAY DIFFRACTION	r_scbond_other	5.397	3.102	9245
X-RAY DIFFRACTION	r_scangle_it	7.744	5.425	13481
X-RAY DIFFRACTION	r_scangle_other	7.744	5.425	13482
X-RAY DIFFRACTION	r_lrange_it	9.425	26.743	20212
X-RAY DIFFRACTION	r_lrange_other	9.441	26.02	20013
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.135	0.05	13492
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.116	0.05	13735

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	0.13544	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.13544	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.11584	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.11584	0.05008

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
2.2-2.257	0.281	566	0.263	10482	0.264	11088	0.955	0.962	99.6393	0.241
2.257-2.319	0.275	544	0.238	10246	0.24	10823	0.96	0.969	99.6951	0.213
2.319-2.386	0.263	491	0.206	10047	0.209	10573	0.963	0.977	99.669	0.179
2.386-2.459	0.234	509	0.191	9675	0.193	10218	0.969	0.98	99.6673	0.163
2.459-2.539	0.222	518	0.166	9407	0.169	9941	0.972	0.985	99.8391	0.141
2.539-2.628	0.235	496	0.165	9132	0.168	9645	0.967	0.984	99.8237	0.141
2.628-2.727	0.212	468	0.158	8793	0.161	9273	0.974	0.985	99.8706	0.136
2.727-2.838	0.211	504	0.157	8466	0.16	8975	0.974	0.986	99.9443	0.136
2.838-2.964	0.203	417	0.156	8143	0.158	8566	0.973	0.986	99.93	0.139
2.964-3.108	0.21	398	0.161	7830	0.163	8229	0.973	0.986	99.9878	0.146
3.108-3.275	0.212	402	0.164	7440	0.167	7844	0.976	0.986	99.9745	0.153
3.275-3.473	0.21	384	0.172	7054	0.174	7438	0.974	0.986	100	0.164
3.473-3.711	0.202	331	0.171	6650	0.173	6982	0.977	0.987	99.9857	0.163
3.711-4.007	0.186	309	0.15	6230	0.152	6539	0.982	0.989	100	0.145
4.007-4.386	0.17	304	0.13	5739	0.132	6043	0.983	0.99	100	0.125
4.386-4.899	0.151	248	0.114	5231	0.116	5479	0.988	0.993	100	0.111
4.899-5.647	0.173	247	0.146	4612	0.147	4859	0.985	0.99	100	0.143
5.647-6.893	0.238	208	0.187	3979	0.19	4187	0.973	0.984	100	0.181
6.893-9.649	0.202	172	0.152	3113	0.154	3285	0.98	0.988	100	0.149
9.649-48.139	0.267	94	0.24	1881	0.242	1975	0.929	0.939	100	0.233

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.9911	-0.0261	-0.332	2.2872	-0.7439	1.5175	0.0596	0.0339	0.1012	-0.1138	0.0039	-0.085	-0.1872	-0.0251	-0.0635	0.1435	-0.0043	0.0338	0.1883	0.1068	0.1284	-25.5792	83.9633	-60.5558
2	1.1761	0.3158	0.0656	1.7771	-0.9907	2.1837	-0.0138	0.0707	0.1847	-0.0304	-0.1008	-0.2175	-0.3199	0.2129	0.1146	0.0829	-0.0202	-0.0013	0.233	0.1106	0.1791	-16.4142	57.461	-29.175
3	1.0595	0.2067	0.1681	1.3493	-0.4787	1.3192	-0.0174	-0.0444	0.078	0.0129	0.042	-0.0869	-0.0648	0.0431	-0.0246	0.0075	0.0212	0.0076	0.1444	0.0386	0.0738	-13.3979	29.3904	3.7582
4	1.6265	-0.0754	-0.322	1.1943	-0.1131	1.6289	-0.0728	-0.3032	-0.0637	0.229	0.1254	0.081	0.096	-0.0731	-0.0526	0.1891	0.0278	0.0003	0.2686	0.14	0.1222	-17.5165	-1.2409	32.3552
5	0.2036	0.2355	-0.2118	2.3006	-2.2715	2.5621	-0.0054	-0.0325	-0.0291	-0.2433	0.2581	0.2777	0.2653	-0.3587	-0.2527	0.1396	0.0175	0.0307	0.3616	0.1131	0.2913	-39.9427	41.8867	-19.0513
6	1.0865	-0.0839	-1.1115	1.0257	0.2271	2.8767	-0.1298	0.0683	-0.3428	-0.0489	0.12	0.163	0.4919	-0.1784	0.0098	0.3679	-0.0173	0.016	0.1961	0.0046	0.3231	-4.4727	57.3773	-91.2589

Refinement TLS group

Selection: ALL

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