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- PDB-6s8l: Structure, Thermodynamics, and Kinetics of Plinabulin Binding to ... -

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Basic information

Entry
Database: PDB / ID: 6s8l
TitleStructure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
Components
  • Designed ankyrin repeat protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-3 chain
KeywordsSTRUCTURAL PROTEIN / Tubulin / Microtubules / Microtubule targeting agents / Cancer
Function / homology
Function and homology information


netrin receptor binding / Post-chaperonin tubulin folding pathway / dorsal root ganglion development / cytoskeleton-dependent intracellular transport / Cargo trafficking to the periciliary membrane / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / Formation of tubulin folding intermediates by CCT/TriC ...netrin receptor binding / Post-chaperonin tubulin folding pathway / dorsal root ganglion development / cytoskeleton-dependent intracellular transport / Cargo trafficking to the periciliary membrane / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / Kinesins / Prefoldin mediated transfer of substrate to CCT/TriC / Assembly and cell surface presentation of NMDA receptors / COPI-independent Golgi-to-ER retrograde traffic / sperm principal piece / COPI-dependent Golgi-to-ER retrograde traffic / intercellular bridge / sperm end piece / Recycling pathway of L1 / ciliary tip / RHOH GTPase cycle / RHO GTPases activate IQGAPs / microtubule-based process / Hedgehog 'off' state / COPI-mediated anterograde transport / cytoplasmic microtubule / Activation of AMPK downstream of NMDARs / peptide binding / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon guidance / Resolution of Sister Chromatid Cohesion / cell periphery / filopodium / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / microtubule cytoskeleton organization / PKR-mediated signaling / mitotic spindle / structural constituent of cytoskeleton / HCMV Early Events / microtubule cytoskeleton / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / cilium / Separation of Sister Chromatids / neuron differentiation / mitotic cell cycle / double-stranded RNA binding / lamellipodium / growth cone / microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cell division / axon / ubiquitin protein ligase binding / neuronal cell body / GTPase activity / dendrite / GTP binding / structural molecule activity / extracellular exosome / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Helix hairpin bin / Ankyrin repeat-containing domain / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin ...Helix hairpin bin / Ankyrin repeat-containing domain / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Helix Hairpins / Alpha Horseshoe / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-PN6 / Tubulin alpha-1B chain / Tubulin beta-3 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsSharma, A. / Olieric, N. / Steinmetz, M.
CitationJournal: Chem / Year: 2019
Title: Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes
Authors: La Sala, G. / Olieric, N.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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-3 chain
F: Designed ankyrin repeat protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7008
Polymers117,3493
Non-polymers1,3515
Water14,178787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-48 kcal/mol
Surface area36400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.630, 91.200, 82.640
Angle α, β, γ (deg.)90.00, 97.49, 90.00
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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBA1B / Cell line (production host): High Five Cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P68363
#2: Protein Tubulin beta-3 chain / Tubulin beta-4 chain / Tubulin beta-III


Mass: 50481.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBB3, TUBB4 / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13509
#3: Protein Designed ankyrin repeat protein (DARPIN) D1


Mass: 16662.904 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 , 5 types, 792 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PN6 / (3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione / Plinabulin


Mass: 336.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy, anticancer, inhibitor*YM
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM Bis-TrisMethane, pH 5.5, supplemented with 200 mM ammonium sulfate and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.801→45.6 Å / Num. obs: 98394 / % possible obs: 93.35 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.39 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1429 / Rpim(I) all: 0.0607 / Rrim(I) all: 0.1555 / Net I/σ(I): 11.04
Reflection shellResolution: 1.801→1.865 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.894 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 5181 / CC1/2: 0.419 / Rpim(I) all: 0.8234 / Rsym value: 2.071 / % possible all: 52.11

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.801→45.6 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.39
RfactorNum. reflection% reflection
Rfree0.2655 4682 5.01 %
Rwork0.2154 --
obs0.2179 93424 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.801→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7777 0 87 787 8651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048079
X-RAY DIFFRACTIONf_angle_d0.72110986
X-RAY DIFFRACTIONf_dihedral_angle_d13.8834781
X-RAY DIFFRACTIONf_chiral_restr0.0471225
X-RAY DIFFRACTIONf_plane_restr0.0051421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8006-1.82110.3567610.3476911X-RAY DIFFRACTION29
1.8211-1.84250.4536890.35221691X-RAY DIFFRACTION53
1.8425-1.8650.3522990.37052281X-RAY DIFFRACTION72
1.865-1.88860.37981500.35612783X-RAY DIFFRACTION87
1.8886-1.91350.41811410.3493066X-RAY DIFFRACTION97
1.9135-1.93970.41971470.34893112X-RAY DIFFRACTION98
1.9397-1.96740.37751750.33943074X-RAY DIFFRACTION98
1.9674-1.99680.4011700.33253079X-RAY DIFFRACTION98
1.9968-2.0280.37351660.33033081X-RAY DIFFRACTION97
2.028-2.06120.34651650.33893023X-RAY DIFFRACTION96
2.0612-2.09670.34821700.34262993X-RAY DIFFRACTION96
2.0967-2.13490.361870.2983006X-RAY DIFFRACTION97
2.1349-2.17590.28011570.25443173X-RAY DIFFRACTION99
2.1759-2.22030.32571720.2413109X-RAY DIFFRACTION99
2.2203-2.26860.31361720.24093080X-RAY DIFFRACTION99
2.2686-2.32140.30211680.23653118X-RAY DIFFRACTION98
2.3214-2.37950.27041850.24293134X-RAY DIFFRACTION99
2.3795-2.44380.30461720.2393112X-RAY DIFFRACTION98
2.4438-2.51570.33061580.25653092X-RAY DIFFRACTION98
2.5157-2.59690.30241620.24063140X-RAY DIFFRACTION99
2.5969-2.68970.2241590.19153133X-RAY DIFFRACTION99
2.6897-2.79740.25441880.18943130X-RAY DIFFRACTION99
2.7974-2.92470.22531710.18373146X-RAY DIFFRACTION99
2.9247-3.07890.21191390.17563207X-RAY DIFFRACTION99
3.0789-3.27170.23321530.17243163X-RAY DIFFRACTION100
3.2717-3.52430.21391520.15773185X-RAY DIFFRACTION100
3.5243-3.87880.21481690.14263158X-RAY DIFFRACTION100
3.8788-4.43970.17591600.13353177X-RAY DIFFRACTION99
4.4397-5.59240.17071530.1453185X-RAY DIFFRACTION98
5.5924-49.21140.20081720.16943200X-RAY DIFFRACTION98
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)
10.9344-0.09630.32771.1126-0.22571.61530.079-0.0243-0.0024-0.0214-0.0426-0.1175-0.00560.423-0.04770.1181-0.03460.02460.2087-0.02580.098244.58682.455117.8059
22.8042-0.94980.15510.3272-0.1521.3538-0.0115-0.05540.0238-0.06410.07190.018-0.33780.0351-0.01760.209-0.04760.06370.0872-0.02460.131531.228311.678813.8415
32.32390.445-0.34122.19230.39522.48150.17440.1698-0.01390.1209-0.090.0999-0.14830.0532-0.0520.1605-0.00960.01690.1378-0.03880.08435.57494.44711.8313
41.8374-0.2995-1.52841.85810.34422.9140.11410.326-0.086-0.089-0.14930.3134-0.1866-0.19930.00480.1456-0.002-0.02370.1935-0.02580.134534.60993.4113-11.7219
51.5392-0.5575-0.64861.56790.97351.61940.01240.3554-0.055-0.0869-0.06880.212-0.39990.1194-0.00140.2281-0.0383-0.06670.2901-0.00020.134439.08636.5199-8.927
60.8408-0.3363-0.320.3573-0.01530.25990.1707-0.03020.1357-0.09030.00620.0763-0.422-0.0636-0.14910.273-0.00790.0730.0941-0.01040.187322.786116.325611.95
71.21151.434-0.2851.8251-0.33631.34810.03310.0162-0.3358-0.2232-0.0061-0.61030.36370.04-0.19390.06550.0345-0.09150.20510.11190.308416.0172-15.835540.3964
85.6767-0.8725-0.54083.09230.36473.69680.04170.3639-0.48690.02250.1283-0.82750.54320.6309-0.01090.21440.0715-0.01340.3186-0.01120.547927.9077-21.374236.7489
91.8497-0.6211-0.59814.47791.15492.4384-0.0486-0.7218-0.53080.2040.2184-0.17910.78110.176-0.10730.2989-0.0054-0.09810.32440.11970.324814.9191-18.995451.1705
102.2243-0.76450.82090.2909-0.16430.567-0.2165-0.97090.20950.54030.1649-0.4061-0.00750.2191-0.08290.16040.0171-0.15130.40330.02390.32214.9578-6.104455.4392
113.4124-0.4402-0.23820.7310.18871.14060.0128-0.18390.22580.03120.0277-0.2645-0.15940.1728-0.02880.0986-0.0226-0.03140.17690.01090.202110.5845-1.904644.0458
121.5880.3189-0.64651.8546-0.4331.38090.0594-0.038-0.2326-0.1216-0.0643-0.13360.09990.0142-0.02850.12970.0243-0.01780.0945-0.00140.1577.3284-9.708231.6176
133.09760.1833-0.65332.43140.50412.673-0.09330.3928-0.5181-0.32430.132-0.09540.5613-0.1408-0.02290.2523-0.0341-0.01590.2593-0.01160.18291.0462-12.072321.8055
141.5901-0.1205-0.36252.78041.10333.34750.00680.6868-0.3394-0.5855-0.0329-0.23610.2870.07530.08080.31460.03970.08420.3316-0.07670.244211.306-10.059914.356
151.13980.1965-0.46770.78550.11931.70090.04440.3848-0.1476-0.1341-0.0486-0.1320.1875-0.2612-0.08290.13680.0121-0.01620.1437-0.0140.17083.1304-3.339327.1081
161.9860.3583-1.32271.5296-1.3594.86280.3097-0.26560.38970.2145-0.0587-0.1212-0.68810.2305-0.18950.1615-0.00240.01260.158-0.03330.2707-1.92088.095343.8001
170.5556-0.4177-0.18842.54692.82115.2041-0.1287-0.16520.0466-0.13520.1882-0.2581-0.44370.89770.05510.2167-0.0288-0.01730.6040.01090.1396-18.72632.083970.0204
185.7531-1.7045-4.39283.80564.25796.00730.0381-0.5031-0.30070.77480.13910.08570.44310.94020.35130.3360.11280.06170.70160.18310.2453-22.0151-6.141173.5224
190.41210.0212-1.17363.0578-0.49693.4970.013-0.4179-0.03520.2433-0.0329-0.1161-0.0320.09890.02330.1049-0.0124-0.00140.29340.03040.0858-22.33881.912263.6108
201.0802-0.5895-0.35031.6660.46981.6822-0.239-0.272-0.28690.22760.01190.13110.28240.0445-0.10510.18170.03060.13050.31850.21260.1859-27.4827-8.088464.2336
213.8438-0.2048-3.3752.9887-1.74626.67560.0725-0.040.3759-0.12420.0993-0.0939-0.25430.0324-0.20660.17040.01410.03410.14370.01770.0885-26.75245.476955.6052
226.96110.4266-0.00622.33281.10724.1063-0.2798-0.1927-0.5110.04350.24360.01410.3018-0.00770.01460.0850.0199-0.00340.1080.00630.0741-23.6433-6.560452.1392
230.8385-0.5037-0.25973.04120.56381.2735-0.0131-0.06220.0386-0.17260.16810.06210.0861-0.1969-0.1620.0823-0.0166-0.00420.16690.0080.0538-23.39910.83745.2276
246.02391.8773-0.17823.36510.57017.5859-0.23630.2681-0.95740.1072-0.09890.14780.6022-0.06570.12770.1802-0.02210.02610.1162-0.03360.1786-24.5857-10.626142.3163
251.2176-0.6237-0.49854.4364-0.87130.76490.1414-0.00060.0222-0.4223-0.0123-0.2546-0.06670.0973-0.09880.1389-0.0031-0.00990.2609-0.02420.076-21.67621.00134.7288
263.7897-3.9644-0.83534.6044-0.12192.3661-0.04510.6738-1.0704-0.69910.13270.39240.6183-0.187-0.03460.2611-0.0514-0.01950.2769-0.0750.2156-20.5592-10.428332.0509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 160 )
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 199 )
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 273 )
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 336 )
5X-RAY DIFFRACTION5chain 'A' and (resid 337 through 372 )
6X-RAY DIFFRACTION6chain 'A' and (resid 373 through 436 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 28 )
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 64 )
9X-RAY DIFFRACTION9chain 'B' and (resid 65 through 88 )
10X-RAY DIFFRACTION10chain 'B' and (resid 89 through 127 )
11X-RAY DIFFRACTION11chain 'B' and (resid 128 through 199 )
12X-RAY DIFFRACTION12chain 'B' and (resid 200 through 273 )
13X-RAY DIFFRACTION13chain 'B' and (resid 274 through 311 )
14X-RAY DIFFRACTION14chain 'B' and (resid 312 through 337 )
15X-RAY DIFFRACTION15chain 'B' and (resid 338 through 401 )
16X-RAY DIFFRACTION16chain 'B' and (resid 402 through 440 )
17X-RAY DIFFRACTION17chain 'F' and (resid 13 through 24 )
18X-RAY DIFFRACTION18chain 'F' and (resid 25 through 35 )
19X-RAY DIFFRACTION19chain 'F' and (resid 36 through 59 )
20X-RAY DIFFRACTION20chain 'F' and (resid 60 through 69 )
21X-RAY DIFFRACTION21chain 'F' and (resid 70 through 82 )
22X-RAY DIFFRACTION22chain 'F' and (resid 83 through 101 )
23X-RAY DIFFRACTION23chain 'F' and (resid 102 through 125 )
24X-RAY DIFFRACTION24chain 'F' and (resid 126 through 134 )
25X-RAY DIFFRACTION25chain 'F' and (resid 135 through 158 )
26X-RAY DIFFRACTION26chain 'F' and (resid 159 through 167 )

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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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