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- PDB-5njh: Triazolopyrimidines stabilize microtubules by binding to the vinc... -

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Basic information

Entry
Database: PDB / ID: 5njh
TitleTriazolopyrimidines stabilize microtubules by binding to the vinca inhibitor site of tubulin
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • tubulin tyrosine ligase TTL
KeywordsSTRUCTURAL PROTEIN / Tubulin / microtubules / microtubule targeting agents / antitumoural / resistance to chemotherapy
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Rossmann fold - #11480 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Tubulin/FtsZ, GTPase domain / Stathmin family ...Rossmann fold - #11480 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / 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 / Dna Ligase; domain 1 / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-8Z8 / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.394 Å
AuthorsSharma, A. / Calvo, G.S. / Prota, A.E. / Diaz, J.F. / Steinmetz, M.O.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Triazolopyrimidines Are Microtubule-Stabilizing Agents that Bind the Vinca Inhibitor Site of Tubulin.
Authors: Saez-Calvo, G. / Sharma, A. / Balaguer, F.A. / Barasoain, I. / Rodriguez-Salarichs, J. / Olieric, N. / Munoz-Hernandez, H. / Berbis, M.A. / Wendeborn, S. / Penalva, M.A. / Matesanz, R. / ...Authors: Saez-Calvo, G. / Sharma, A. / Balaguer, F.A. / Barasoain, I. / Rodriguez-Salarichs, J. / Olieric, N. / Munoz-Hernandez, H. / Berbis, M.A. / Wendeborn, S. / Penalva, M.A. / Matesanz, R. / Canales, A. / Prota, A.E. / Jimenez-Barbero, J. / Andreu, J.M. / Lamberth, C. / Steinmetz, M.O. / Diaz, J.F.
History
DepositionMar 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: tubulin tyrosine ligase TTL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,28817
Polymers261,3056
Non-polymers2,98311
Water6,503361
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23400 Å2
ΔGint-137 kcal/mol
Surface area78220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.430, 158.353, 173.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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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: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (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 (cattle) / References: UniProt: Q6B856
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


Mass: 16844.162 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 TTL


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: E1BQ43

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Non-polymers , 6 types, 372 molecules

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


Mass: 523.180 Da / Num. of mol.: 2 / 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-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Chemical ChemComp-8Z8 / 5-chloranyl-7-[(1~{R},5~{S})-3-methoxy-8-azabicyclo[3.2.1]octan-8-yl]-6-[2,4,6-tris(fluoranyl)phenyl]-[1,2,4]triazolo[1,5-a]pyrimidine


Mass: 423.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17ClF3N5O
#9: 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
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 10% PEG 4K, 20% glycerol, 30 mM CaCl2, 30 mM MgCl2, 0.1 M MES/imidazole, pH 6.7, 1 mM AMPPCP, 10 mM DTT, 0.1 mM GDP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.394→48.09 Å / Num. obs: 112238 / % possible obs: 99.7 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 18.6
Reflection shellResolution: 2.394→2.479 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 1.27 / % possible all: 96.76

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Processing

Software
NameVersionClassification
PHENIX(dev_2420: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4I4T

4i4t


Resolution: 2.394→48.086 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 2000 1.78 %
Rwork0.2175 --
obs0.2178 112225 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.394→48.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17177 0 185 361 17723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917845
X-RAY DIFFRACTIONf_angle_d1.42524225
X-RAY DIFFRACTIONf_dihedral_angle_d22.7876614
X-RAY DIFFRACTIONf_chiral_restr0.1482646
X-RAY DIFFRACTIONf_plane_restr0.0083139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3939-2.45380.36731360.35147455X-RAY DIFFRACTION95
2.4538-2.52010.32641420.31557835X-RAY DIFFRACTION100
2.5201-2.59430.32361410.30277822X-RAY DIFFRACTION100
2.5943-2.6780.33351410.29487786X-RAY DIFFRACTION100
2.678-2.77370.30541430.28547836X-RAY DIFFRACTION100
2.7737-2.88470.27251420.27627856X-RAY DIFFRACTION100
2.8847-3.0160.30121420.27097833X-RAY DIFFRACTION100
3.016-3.1750.2581430.25287844X-RAY DIFFRACTION100
3.175-3.37390.24041430.23517909X-RAY DIFFRACTION100
3.3739-3.63430.24221430.21837868X-RAY DIFFRACTION100
3.6343-3.99980.20841440.18797909X-RAY DIFFRACTION100
3.9998-4.57820.21241440.17097979X-RAY DIFFRACTION100
4.5782-5.76660.19841460.18328009X-RAY DIFFRACTION100
5.7666-48.09540.19961500.18938284X-RAY DIFFRACTION100
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)
11.5402-0.0501-0.20414.36590.7612.01080.07370.04820.295-0.2880.1932-0.0959-0.37270.2376-0.26070.4446-0.0760.10370.4626-0.10130.450730.150288.803448.7894
21.51230.0515-0.94882.7280.08422.31260.14450.01520.24230.22370.01630.3152-0.2545-0.0572-0.14420.40820.00660.06410.3879-0.06980.452618.267182.331562.7676
31.0166-0.1986-0.20684.93631.14642.13470.0605-0.11060.32190.74270.08360.2209-0.11070.024-0.14310.4801-0.02470.13170.4807-0.09550.51917.194283.733370.2557
41.07260.0935-0.62032.3963.16418.11350.0078-0.1433-0.13180.17420.2075-0.25280.33840.856-0.22690.41960.0766-0.03150.4671-0.05230.451332.072462.721458.3893
56.7504-1.5695-1.29357.1607-0.12943.50190.32340.35950.7928-0.4557-0.22180.1074-0.7253-0.2208-0.05960.5280.03220.00880.40020.04750.380616.33168.91216.2591
61.05390.0929-0.61297.3703-0.74721.1017-0.00580.12760.1185-0.56180.1086-0.2104-0.26820.1272-0.10980.5279-0.03680.04050.548-0.02640.443329.940855.68912.5385
72.6391.45140.86224.12491.68913.0304-0.0079-0.06120.1103-0.02480.1105-0.2479-0.18560.2019-0.10870.34770.02660.03930.3802-0.040.333725.029752.641324.259
83.24091.54463.70564.82381.70536.86930.1948-0.54140.45220.0737-0.51891.0360.184-0.89960.30980.39680.02610.04080.4477-0.15720.5215.830251.270525.2631
92.4530.1552.59651.44360.67332.9602-0.1513-0.50710.1693-0.2001-0.02570.3285-0.311-0.44680.1660.45170.00130.05650.5053-0.08820.480611.848661.243233.3007
103.0938-0.43011.91772.5776-1.21774.7749-0.2038-0.25680.20520.17040.03950.2798-0.3624-1.07180.13850.46640.04920.04330.6255-0.1340.47126.294160.364541.8454
110.4886-1.0306-1.31184.66264.79675.3124-0.0330.01460.03380.7144-0.17170.41240.5773-0.16620.22930.4233-0.05940.06880.4598-0.05740.333116.717441.63832.4689
121.0809-0.8115-0.71444.69384.98729.8044-0.0085-0.0977-0.0390.70610.2294-0.29050.65430.5919-0.24150.431-0.0062-0.05780.38530.01550.424127.30737.951929.4086
131.9066-0.89790.01113.1633-0.03261.7014-0.01990.14160.1436-0.2612-0.0049-0.0429-0.26390.07470.02050.358-0.06150.00680.3629-0.00750.316421.963332.5491-12.2721
140.393-0.04270.26241.25360.72871.2466-0.05020.00350.01730.0086-0.06810.20830.0406-0.18190.11410.3385-0.04780.02010.3932-0.03240.39410.665725.61063.1404
155.3672-2.4861-0.09887.5064-0.35531.731-0.07590.64920.1743-0.6240.12870.0674-0.11290.0736-0.05660.4651-0.0720.03780.66030.01760.245417.44599.5719-44.4731
162.16820.1201-0.58952.11050.19491.699-0.06040.3911-0.1006-0.23820.1342-0.14680.02440.0748-0.06580.4025-0.02970.040.5695-0.11430.356921.4845-2.1552-34.093
172.1068-0.63690.22272.4189-0.85582.1911-0.11920.1946-0.27880.13870.07650.2934-0.067-0.24950.04240.373-0.04220.0560.4471-0.07160.346610.4913-4.0348-21.254
184.98760.4901-2.37561.9395-0.88753.4376-0.3997-0.0243-0.6540.00080.1213-0.16920.75540.70520.10020.42520.0721-0.01780.4459-0.11980.536431.4833-16.6069-25.112
191.9345-1.69960.63094.1873-0.47750.337-0.0354-0.0006-0.05411.50350.31060.30750.02380.3124-0.29711.1921-0.06320.07140.6565-0.2450.707425.270493.702978.8948
200.1443-0.0563-0.25374.19644.46045.0265-0.0852-0.0186-0.04410.25730.4996-0.47760.36440.6047-0.49850.41370.01450.04320.5604-0.12370.596343.858529.19573.5346
211.99542.95780.11296.66531.32340.9723-0.67210.5066-0.6707-0.43220.143-0.21281.1919-0.28960.27191.0572-0.17740.30330.6096-0.16630.63576.203254.411267.3725
224.57181.24770.33162.3516-0.53564.4599-0.0758-0.5428-0.61670.2457-0.3365-0.93760.21530.98580.3840.58740.08310.00670.75260.18850.880513.726359.2684103.5333
232.12211.1239-1.6892.11-0.6643.3813-0.44630.1217-0.6641-0.18480.169-0.23610.7161-0.19110.12870.6024-0.00010.14250.40830.00020.6067-2.566654.185690.6844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 180)
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 311)
3X-RAY DIFFRACTION3chain 'A' and (resid 312 through 401)
4X-RAY DIFFRACTION4chain 'A' and (resid 402 through 436)
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 88)
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 127)
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 197)
8X-RAY DIFFRACTION8chain 'B' and (resid 198 through 223)
9X-RAY DIFFRACTION9chain 'B' and (resid 224 through 295)
10X-RAY DIFFRACTION10chain 'B' and (resid 296 through 373)
11X-RAY DIFFRACTION11chain 'B' and (resid 374 through 401)
12X-RAY DIFFRACTION12chain 'B' and (resid 402 through 437)
13X-RAY DIFFRACTION13chain 'C' and (resid 2 through 197)
14X-RAY DIFFRACTION14chain 'C' and (resid 198 through 440)
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 88)
16X-RAY DIFFRACTION16chain 'D' and (resid 89 through 295)
17X-RAY DIFFRACTION17chain 'D' and (resid 296 through 401)
18X-RAY DIFFRACTION18chain 'D' and (resid 402 through 441)
19X-RAY DIFFRACTION19chain 'E' and (resid 6 through 46)
20X-RAY DIFFRACTION20chain 'E' and (resid 47 through 141)
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 66)
22X-RAY DIFFRACTION22chain 'F' and (resid 69 through 198)
23X-RAY DIFFRACTION23chain 'F' and (resid 199 through 380)

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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