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- PDB-7alr: Crystal structure of TD1-gatorbulin1 complex -

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Basic information

Entry
Database: PDB / ID: 7alr
TitleCrystal structure of TD1-gatorbulin1 complex
Components
  • Designed Ankyrin Repeat Protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-3 chain
KeywordsSTRUCTURAL PROTEIN / tubulin / gatorbulin / antitumoral / microtubule
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 / GLYCINE / GUANOSINE-5'-TRIPHOSPHATE / Chem-RQK / Tubulin alpha-1B chain / Tubulin beta-3 chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsOliva, M.A. / Diaz, J.F.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-104545RB-I00 Spain
Spanish National Research Council201920E111 Spain
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Gatorbulin-1, a distinct cyclodepsipeptide chemotype, targets a seventh tubulin pharmacological site.
Authors: Matthew, S. / Chen, Q.Y. / Ratnayake, R. / Fermaintt, C.S. / Lucena-Agell, D. / Bonato, F. / Prota, A.E. / Lim, S.T. / Wang, X. / Diaz, J.F. / Risinger, A.L. / Paul, V.J. / Oliva, M.A. / Luesch, H.
History
DepositionOct 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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: 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)121,92813
Polymers119,9113
Non-polymers2,01810
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-65 kcal/mol
Surface area36620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.462, 91.292, 82.970
Angle α, β, γ (deg.)90.000, 97.440, 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, 394 molecules

#4: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-RQK / (2~{R})-2-oxidanyl-2-[(6~{S},9~{S},12~{S},15~{S},17~{S})-6,10,12,17-tetramethyl-3-methylidene-7-oxidanyl-2,5,8,11,14-pentakis(oxidanylidene)-13-oxa-1,4,7,10-tetrazabicyclo[13.3.0]octadecan-9-yl]ethanamide


Mass: 483.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N5O9 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: 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
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 46.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris Methane pH 5.5, 0.20 Ammonium Sulfate, 18-22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.93→49.21 Å / Num. obs: 81042 / % possible obs: 99.4 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.032 / Rrim(I) all: 0.072 / Net I/σ(I): 13.1 / Num. measured all: 397791 / Scaling rejects: 33
Reflection shell

Diffraction-ID: 1 / % possible all: 98.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.93-1.9750.4942174943640.9310.2440.5512.7
10.03-49.214.70.03529036130.9970.0180.03932.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NM5

5nm5


Resolution: 1.93→49.208 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 4072 5.03 %
Rwork0.1677 76894 -
obs0.1695 80966 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.17 Å2 / Biso mean: 40.059 Å2 / Biso min: 16.99 Å2
Refinement stepCycle: final / Resolution: 1.93→49.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7847 0 201 384 8432
Biso mean--31.19 34.17 -
Num. residues----1008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.93-1.95270.32031550.2656257898
1.9527-1.97650.30671340.2427260598
1.9765-2.00150.32341270.2345262998
2.0015-2.02790.29371610.2242265699
2.0279-2.05570.26971160.2205260899
2.0557-2.0850.26351540.2031261099
2.085-2.11620.25041670.2038259099
2.1162-2.14920.26581290.197265299
2.1492-2.18450.23411360.193264699
2.1845-2.22210.20971280.1884265299
2.2221-2.26250.24111190.1829265199
2.2625-2.3060.20731360.1812266099
2.306-2.35310.24551330.1835263999
2.3531-2.40430.21841510.1711264499
2.4043-2.46020.21931480.1758263399
2.4602-2.52170.21931430.1682265299
2.5217-2.58990.19911410.1733266199
2.5899-2.66610.18721350.16362658100
2.6661-2.75220.20721480.1715264899
2.7522-2.85050.2251520.1741262599
2.8505-2.96460.21111480.1725266099
2.9646-3.09950.22471480.17212656100
3.0995-3.26290.19291240.17922692100
3.2629-3.46730.20811410.1662684100
3.4673-3.73490.17641140.1562690100
3.7349-4.11060.18131370.13772696100
4.1106-4.7050.151490.12732680100
4.705-5.92630.17481490.14672707100
5.9263-49.2080.1861490.1694273299

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