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- PDB-7odn: Crystal structure of TD1-mebendazole complex -

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Basic information

Entry
Database: PDB / ID: 7odn
TitleCrystal structure of TD1-mebendazole complex
Components
  • Designed Ankyrin Repeat Protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-3 chain
KeywordsSTRUCTURAL PROTEIN / Tubulin / Colchicine / Mebendazole
Function / homology
Function and homology information


Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / netrin receptor binding / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / netrin receptor binding / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic / netrin-activated signaling pathway / RHO GTPases activate IQGAPs / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases Activate Formins / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / dorsal root ganglion development / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Recruitment of NuMA to mitotic centrosomes / Hedgehog 'off' state / intercellular bridge / cytoplasmic microtubule / cellular response to interleukin-4 / filopodium / cell periphery / axon guidance / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / microtubule cytoskeleton / double-stranded RNA binding / lamellipodium / mitotic cell cycle / growth cone / microtubule / GTPase activity / dendrite / neuronal cell body / ubiquitin protein ligase binding / GTP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-V95 / Tubulin alpha-1B chain / Tubulin beta-3 chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsOliva, M.A. / Bonato, F. / Diaz, J.F.
Funding support Spain, European Union, 3items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-104545RB-I00/AEI/10.13039/501100011033 Spain
Spanish National Research CouncilFondo de Investigaciones Sanitarias COV20/01007 Spain
European Research Council (ERC)H2020-MSCA-ITN-2019 860070 TUBINTRAINEuropean Union
CitationJournal: Int J Mol Sci / Year: 2022
Title: Effect of Clinically Used Microtubule Targeting Drugs on Viral Infection and Transport Function.
Authors: Oliva, M.A. / Tosat-Bitrian, C. / Barrado-Gil, L. / Bonato, F. / Galindo, I. / Garaigorta, U. / Alvarez-Bernad, B. / Paris-Ogayar, R. / Lucena-Agell, D. / Gimenez-Abian, J.F. / Garcia- ...Authors: Oliva, M.A. / Tosat-Bitrian, C. / Barrado-Gil, L. / Bonato, F. / Galindo, I. / Garaigorta, U. / Alvarez-Bernad, B. / Paris-Ogayar, R. / Lucena-Agell, D. / Gimenez-Abian, J.F. / Garcia-Dorival, I. / Urquiza, J. / Gastaminza, P. / Diaz, J.F. / Palomo, V. / Alonso, C.
History
DepositionApr 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-3 chain
F: Designed Ankyrin Repeat Protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,93216
Polymers119,9113
Non-polymers2,02113
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-122 kcal/mol
Surface area36390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.441, 91.390, 82.671
Angle α, β, γ (deg.)90.000, 97.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ABF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-3 chain


Mass: 50481.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2T9S0
#3: Protein Designed Ankyrin Repeat Protein (DARPIN) D1


Mass: 19224.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 8 types, 122 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-V95 / methyl N-(6-benzoyl-1H-benzimidazol-2-yl)carbamate / Mebendazole / 4030 / Mebendazole


Mass: 295.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13N3O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: bis-tris methane, ammonium sulphate,PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 2.33→49.11 Å / Num. obs: 45660 / % possible obs: 98.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 40.84 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.045 / Rrim(I) all: 0.093 / Net I/σ(I): 11.9 / Num. measured all: 189889 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.33-2.414.20.7961854744180.8650.4410.9131.897.9
9.02-49.113.90.02532358250.9990.0140.02940.998.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.79 Å49.11 Å
Translation6.79 Å49.11 Å

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Processing

Software
NameVersionClassification
PHENIX1.16.refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nm5

5nm5


Resolution: 2.33→49.11 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 2193 4.81 %
Rwork0.1902 43379 -
obs0.192 45572 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.69 Å2 / Biso mean: 51.1507 Å2 / Biso min: 24.41 Å2
Refinement stepCycle: final / Resolution: 2.33→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7836 0 170 109 8115
Biso mean--49.98 41.91 -
Num. residues----1007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.33-2.380.34351250.29052658278397
2.38-2.440.32821300.29482695282598
2.44-2.50.31741380.28972669280798
2.5-2.560.32371420.26912680282298
2.56-2.640.30351370.24182663280098
2.64-2.730.25011330.23112722285598
2.73-2.820.31231280.2332712284098
2.82-2.940.25931290.23792725285498
2.94-3.070.30021420.25332689283198
3.07-3.230.28831480.22042708285699
3.23-3.430.23331270.2022711283898
3.43-3.70.22451280.18762730285899
3.7-4.070.19761450.15222730287599
4.07-4.660.1641500.13342737288799
4.66-5.870.17331340.14632775290999
5.87-49.110.18821570.15852775293298
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)
10.0383-0.0111-0.06430.160.02950.0349-0.2026-0.0028-0.5474-0.42780.0329-0.33670.42860.18750.00020.29680.07760.03250.43650.0930.3449-23.219312.46662.2889
20.0128-0.00520.00260.04180.04970.03460.1174-0.11590.08470.1133-0.0405-0.0247-0.08360.108100.43460.03930.06180.49490.03160.3636-26.321723.346655.8285
3-0.00020.0174-0.0130.0050.01810.0459-0.0788-0.001-0.45040.24470.045-0.01660.38060.244400.387-0.00250.02310.42630.05090.4163-23.158511.311552.2969
40.12410.02040.14930.07380.07560.1422-0.06170.06010.08050.08210.07050.1905-0.0261-0.219-00.33820.03010.0020.42270.00470.3879-22.885818.600845.431
50.0137-0.02610.00410.0310.010.0383-0.27130.0456-0.3392-0.0794-0.0671-0.08610.55450.0161-0.00010.47890.0343-0.04510.4492-0.07060.5414-247.265842.4624
60.0926-0.0740.0670.0675-0.01130.0844-0.1283-0.2434-0.03120.0512-0.18080.1102-0.2877-0.1705-0.00010.44880.0275-0.03020.46390.02330.4353-24.939121.248637.1738
70.0085-0.0098-0.0140.00860.0080.00890.1584-0.21680.0762-0.2474-0.0078-0.07020.00810.0741-00.46240.0085-0.00450.4637-0.03810.4312-16.325815.814732.1823
80.0055-0.00960.01560.0246-0.00790.02150.01760.1573-0.0253-0.5763-0.16350.15470.27510.36220.00020.42340.0085-0.05610.4481-0.00190.4114-20.1637.415132.234
90.70460.0293-0.18840.78690.07791.4960.0346-0.0142-0.0122-0.012-0.0351-0.0074-0.08450.1189-00.3146-0.0294-0.00340.2855-0.01510.302940.143321.053414.4516
101.0207-0.0854-0.39890.43130.07331.3380.06260.13650.0215-0.0619-0.01520.0246-0.13390.01100.3783-0.0068-0.00160.25740.01480.322232.53128.2229-0.9409
110.3963-0.25340.34340.30750.04870.5353-0.0559-0.1588-0.3560.06610.0136-0.12060.17990.1729-00.42970.03150.00180.45970.15490.622720.6735-1.107141.5944
12-0.0017-0.0477-0.00540.20560.18410.15090.008-0.4763-0.0220.5431-0.2149-0.0546-0.10590.0843-0.01080.4460.0069-0.05270.77880.13210.501415.479411.795455.2767
130.29470.1982-0.42070.03940.10860.70280.0157-0.1415-0.0711-0.0209-0.03480.0074-0.0370.0742-00.37810.0075-0.02320.4520.04670.46157.707513.749642.1617
140.45380.20630.18060.1642-0.2620.5178-0.00020.0259-0.25420.00060.0333-0.14190.09050.1275-00.42550.00780.02860.37620.03030.502211.46148.354530.7922
150.1278-0.03320.0870.1611-0.12890.23030.05950.0424-0.0752-0.0627-0.128-0.2320.0864-0.2481-00.4017-0.00470.01870.42420.00520.43522.29876.239223.3207
160.09170.1164-0.02290.1701-0.06520.05110.05690.22230.0847-0.2092-0.0171-0.33420.0714-0.187500.51170.02920.03320.44220.00680.478510.90098.435314.0382
170.48420.34320.08640.16320.0120.3692-0.0010.1504-0.1657-0.0455-0.0545-0.0620.0623-0.1666-00.40710.0223-0.00030.39350.02680.38863.972214.551926.9245
180.3666-0.00530.01150.28010.22480.13980.2556-0.06120.12450.1029-0.068-0.0269-0.473-0.11930.00010.4282-0.02830.00320.47980.04810.4687-1.891126.529543.0903
190.0056-0.02750.01020.0411-0.01210.0017-0.33480.0466-0.26270.21540.07270.1039-0.30580.293900.46880.0022-0.01580.72070.05190.3296-18.270420.057170.0758
200.01580.00470.0180.00220.0060.01890.09710.0409-0.33340.0786-0.05650.1866-0.26550.2170.00010.65620.11750.04150.72810.17280.5518-21.989112.320374.1076
210.0184-0.0275-0.00240.04890.02820.0184-0.176-0.22670.1878-0.11730.16830.2655-0.1141-0.043-00.423-0.01670.09770.4873-0.02660.4352-23.978924.097265.3481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 50 through 69 )F50 - 69
2X-RAY DIFFRACTION2chain 'F' and (resid 70 through 82 )F70 - 82
3X-RAY DIFFRACTION3chain 'F' and (resid 83 through 101 )F83 - 101
4X-RAY DIFFRACTION4chain 'F' and (resid 102 through 125 )F102 - 125
5X-RAY DIFFRACTION5chain 'F' and (resid 126 through 134 )F126 - 134
6X-RAY DIFFRACTION6chain 'F' and (resid 135 through 148 )F135 - 148
7X-RAY DIFFRACTION7chain 'F' and (resid 149 through 158 )F149 - 158
8X-RAY DIFFRACTION8chain 'F' and (resid 159 through 167 )F159 - 167
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 243 )A1 - 243
10X-RAY DIFFRACTION10chain 'A' and (resid 244 through 435 )A244 - 435
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 88 )B2 - 88
12X-RAY DIFFRACTION12chain 'B' and (resid 89 through 127 )B89 - 127
13X-RAY DIFFRACTION13chain 'B' and (resid 128 through 215 )B128 - 215
14X-RAY DIFFRACTION14chain 'B' and (resid 216 through 266 )B216 - 266
15X-RAY DIFFRACTION15chain 'B' and (resid 267 through 311 )B267 - 311
16X-RAY DIFFRACTION16chain 'B' and (resid 312 through 338 )B312 - 338
17X-RAY DIFFRACTION17chain 'B' and (resid 339 through 400 )B339 - 400
18X-RAY DIFFRACTION18chain 'B' and (resid 401 through 441 )B401 - 441
19X-RAY DIFFRACTION19chain 'F' and (resid 13 through 24 )F13 - 24
20X-RAY DIFFRACTION20chain 'F' and (resid 25 through 36 )F25 - 36
21X-RAY DIFFRACTION21chain 'F' and (resid 37 through 49 )F37 - 49

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