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- PDB-7pje: Inhibiting parasite proliferation using a rationally designed ant... -

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Basic information

Entry
Database: PDB / ID: 7pje
TitleInhibiting parasite proliferation using a rationally designed anti-tubulin agent
Components
  • Darpin D1
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / Tubulin / Microtubules / Protozoa / Apicomplexa
Function / homology
Function and homology information


microtubule-based process / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
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/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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha chain / Tubulin beta chain
Similarity search - Component
Biological speciessynthetic construct (others)
Tetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSharma, A. / Gaillard, N. / Ehrhard, V.A. / Steinmetz, M.O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Novartis FreeNovation Switzerland
CitationJournal: Embo Mol Med / Year: 2021
Title: Inhibiting parasite proliferation using a rationally designed anti-tubulin agent.
Authors: Gaillard, N. / Sharma, A. / Abbaali, I. / Liu, T. / Shilliday, F. / Cook, A.D. / Ehrhard, V. / Bangera, M. / Roberts, A.J. / Moores, C.A. / Morrissette, N. / Steinmetz, M.O.
History
DepositionAug 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 3, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / pdbx_data_processing_status / pdbx_database_proc
Item: _atom_site_anisotrop.id / _citation.page_first ..._atom_site_anisotrop.id / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.1Nov 17, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume
Revision 2.2Jan 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 chain
B: Tubulin beta chain
F: Darpin D1
C: Tubulin alpha chain
D: Tubulin beta chain
E: Darpin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,55013
Polymers231,3856
Non-polymers2,1667
Water18,9701053
1
A: Tubulin alpha chain
B: Tubulin beta chain
F: Darpin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7877
Polymers115,6923
Non-polymers1,0954
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-49 kcal/mol
Surface area35660 Å2
MethodPISA
2
C: Tubulin alpha chain
D: Tubulin beta chain
E: Darpin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7636
Polymers115,6923
Non-polymers1,0713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-40 kcal/mol
Surface area35690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.130, 183.920, 118.323
Angle α, β, γ (deg.)90.000, 92.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules ACBDFE

#1: Protein Tubulin alpha chain / Alpha-tubulin


Mass: 49639.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: P41351
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49617.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: P41352
#3: Protein Darpin D1


Mass: 16435.645 Da / Num. of mol.: 2
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 , 3 types, 1060 molecules

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


Mass: 523.180 Da / Num. of mol.: 4 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1053 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M sodium sulfate, 10% DMSO and 18 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→46.83 Å / Num. obs: 219447 / % possible obs: 98.37 % / Redundancy: 5.9 % / Biso Wilson estimate: 30.28 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07281 / Rpim(I) all: 0.03267 / Rrim(I) all: 0.08004 / Net I/σ(I): 12.84
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 6 % / Rmerge(I) obs: 1.177 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 20372 / CC1/2: 0.796 / CC star: 0.942 / Rpim(I) all: 0.5162 / % possible all: 91.63

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DRX

4drx


Resolution: 1.75→46.83 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 10963 5 %
Rwork0.1815 208337 -
obs0.1831 219300 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 271.08 Å2 / Biso mean: 49.6015 Å2 / Biso min: 20.54 Å2
Refinement stepCycle: final / Resolution: 1.75→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15067 0 169 1053 16289
Biso mean--35.27 48.28 -
Num. residues----1946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.37142890.3625494578378
1.77-1.790.35793680.34116983735198
1.79-1.810.34213600.31846851721198
1.81-1.840.31953640.30346914727899
1.84-1.860.32843700.27817018738899
1.86-1.890.29963630.27156893725699
1.89-1.910.30543670.26166960732798
1.91-1.940.28033690.25446985735499
1.94-1.970.28153630.24226880724399
1.97-20.2863700.23817034740499
2-2.040.26673640.22096908727299
2.04-2.080.24543670.2097010737799
2.08-2.120.23863660.20396952731899
2.12-2.160.22693670.19327007737499
2.16-2.210.23223650.18856936730199
2.21-2.260.22613710.18747051742299
2.26-2.310.21953660.17956951731799
2.31-2.380.21243720.18327068744099
2.38-2.450.22523660.1826934730099
2.45-2.520.22523690.18847025739499
2.52-2.610.25133720.19087053742599
2.61-2.720.21993680.182269877355100
2.72-2.840.22353690.18270137382100
2.84-2.990.21273710.189470407411100
2.99-3.180.22193720.184970697441100
3.18-3.430.1973710.172270527423100
3.43-3.770.18763720.160770637435100
3.77-4.320.17693690.14267035740499
4.32-5.440.15983710.13657029740099
5.44-46.830.20673720.183271427514100
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)
10.49550.1209-0.02381.4823-2.21974.09330.0216-0.4046-0.14360.4145-0.05320.16640.268-0.65510.2030.3454-0.04680.03880.52050.00330.38968.6696-21.806676.8876
22.469-0.0746-0.21070.87810.14172.09380.1038-0.2548-0.06850.135-0.0990.23990.0436-0.57320.05490.25610.0030.03050.4141-0.050.30126.0279-16.63169.2132
31.76360.42160.55711.5481-0.47552.50530.08-0.227-0.13620.0285-0.02240.0590.20750.0191-0.12670.30460.0190.02170.3723-0.02310.274323.4964-19.123979.1446
40.8540.20430.51680.2950.72682.6876-0.0324-0.19370.06150.07410.0227-0.0524-0.10740.2627-0.02110.29040.03050.03260.3204-0.06210.33227.049-11.356674.9699
51.5528-0.26570.18821.7999-0.53421.2433-0.0283-0.3667-0.40470.3504-0.00390.250.1774-0.2104-0.01140.2145-0.06710.01440.31340.03480.38285.1588-39.878841.8224
62.04770.1019-0.55381.1622-0.11631.76560.01440.3008-0.1358-0.1024-0.02990.19170.1357-0.4793-0.03690.25360.015-0.03560.3671-0.02850.3266.0057-27.611127.314
71.53360.56030.68121.4599-0.68771.21510.04810.018-0.2989-0.0889-0.0525-0.05780.2447-0.0135-0.03980.17380.0084-0.01780.19790.01060.297520.5477-34.395536.4988
81.3599-0.26210.25851.4553-0.08220.87780.1345-0.1505-0.38920.1065-0.0653-0.26820.1760.3048-0.01110.2969-0.0128-0.01420.35590.0090.432429.9255-32.403543.2619
90.7398-0.04850.33290.83880.54721.31690.0416-0.057-0.12840.0883-0.0053-0.0574-0.13420.13470.05670.1905-0.00330.01160.3005-0.00310.314327.6658-26.332236.688
100.8889-0.6131-0.34961.03680.19470.9549-0.01730.19810.0136-0.36990.02740.1274-0.6029-0.0642-0.21950.3663-0.01680.01210.30080.03280.295721.2178-14.057621.7283
110.6408-0.0708-0.01720.3051-0.16490.2082-0.05920.18510.9491-0.2881-0.09970.2829-1.06690.01530.25570.51380.0519-0.04650.6257-0.04590.487114.5152-18.9524-9.4791
120.44570.45310.32162.25981.90511.6493-0.20530.0717-0.4589-0.6948-0.30010.7213-0.1504-0.55320.02510.6348-0.0261-0.08610.597-0.06030.533113.5605-26.9113-14.9553
131.25820.0721-0.2040.5798-0.64711.2489-0.00210.1364-0.055-0.1488-0.005-0.0544-0.0650.27360.03320.38770.00660.04280.3792-0.0360.261128.3836-23.652-2.4733
141.111-0.48720.31560.22420.14684.61-0.1575-0.0982-0.27740.0155-0.1129-0.46670.13910.28010.12490.4130.16220.0250.5822-0.0580.485338.264-32.68974.9629
152.9712-0.4072-1.09241.3367-0.21060.93960.01330.59120.168-0.3004-0.09640.06510.0246-0.6412-0.21030.26580.0563-0.0070.44740.0150.28313.135823.1897-20.3163
160.33540.0067-0.06090.01520.03890.180.04240.5228-0.0624-0.1609-0.16760.0539-0.1386-0.5985-0.1680.39080.1419-0.06350.8350.07360.43645.146426.3042-29.7617
170.5534-0.0872-0.53340.2442-0.43741.21840.0774-0.0067-0.03010.0941-0.04420.01970.0007-0.49240.0020.2431-0.0006-0.00320.4558-0.08920.295610.914916.7533-8.8725
180.2759-0.13-0.20330.1857-0.19870.4470.05060.104-0.2070.16610.1213-0.3455-0.12720.12400.3633-0.0427-0.01160.2899-0.06540.301230.515325.5639-12.3021
190.16190.03230.04150.1288-0.13930.17470.07430.41580.0604-0.17230.0278-0.12580.0178-0.1804-00.34180.03190.00060.42030.01710.350721.292818.4141-24.9322
200.2563-0.12650.20560.11280.2450.6483-0.01280.0549-0.0580.0183-0.0326-0.0667-0.08120.070900.2934-0.0362-0.00890.35-0.03990.307934.853118.1051-21.4048
210.15280.02610.12340.22070.22760.2250.11810.1828-0.05730.0967-0.06520.08-0.01190.27700.3229-0.0058-0.00330.4404-0.02790.310535.898416.2972-33.6077
22-0.03230.1738-0.01760.2415-0.21680.45870.12850.20070.01320.0194-0.1879-0.1616-0.08250.159-00.42550.0275-0.04530.4494-0.05820.355732.057818.008-28.9927
230.46460.16630.26910.28060.4430.67370.0035-0.0128-0.08980.1016-0.0242-0.0290.2330.1368-00.34790.00660.00070.2709-0.04790.308228.09658.2324-2.8945
240.27540.15710.12160.2553-0.18610.3766-0.10670.00020.1514-0.1099-0.10140.2185-0.329-0.4716-0.08450.5330.2372-0.13160.3991-0.09720.45097.524842.047615.2276
250.02770.0123-0.05490.2406-0.02680.1093-0.0896-0.18350.17010.0615-0.04620.194-0.3336-0.378-0.11440.60410.2775-0.03640.6056-0.20710.56983.07942.402729.5591
260.7180.37840.51340.91630.72120.64430.2245-0.3945-0.01110.2603-0.23930.38890.2208-1.0165-0.00130.26110.18480.03270.6773-0.17770.44240.510729.744133.4119
270.9340.1177-0.35091.009-0.02020.99190.0127-0.05160.03150.041-0.0370.0312-0.1799-0.2344-00.34090.0686-0.02820.2996-0.06710.281717.071429.674124.9716
280.65150.09170.62720.06940.02330.78110.12910.0916-0.1088-0.04540.0020.0587-0.10330.70970.00750.5377-0.09020.01520.3063-0.04390.383932.922440.206517.9388
290.073-0.0128-0.04860.02890.01310.02180.1575-0.03420.0096-0.1311-0.0303-0.1066-0.00540.0751-00.44670.0331-0.01230.3253-0.07380.322231.175631.836416.2933
300.2242-0.08160.09950.46510.32150.2354-0.0011-0.02480.0158-0.0404-0.044-0.07550.03220.2373-00.37730.0327-0.02620.3425-0.03080.310930.861828.973518.3901
310.33220.32090.27370.40640.20160.19730.0428-0.0901-0.09740.1505-0.11520.0750.3830.0195-00.46650.0164-0.00080.3981-0.04780.357721.07615.949836.6443
320.0868-0.0187-0.03890.1132-0.0640.02510.0450.20560.09210.56160.28770.5934-0.2557-0.18070.00010.43860.00290.03560.5538-0.01530.486211.977125.477669.1011
330.1908-0.0859-0.02550.1518-0.20210.36140.0352-0.11380.049-0.0152-0.0543-0.03180.12480.129100.47140.0204-0.03450.3694-0.04890.294123.307324.260564.1782
340.02350.0415-0.00930.03780.00240.0123-0.2945-0.05590.23580.245-0.2487-0.0964-0.1923-0.15700.4774-0.0186-0.04970.4719-0.0620.393929.721234.667961.95
350.09590.0799-0.07360.1868-0.01650.0834-0.0101-0.08910.0768-0.0607-0.0239-0.03150.27640.533900.43230.0425-0.0050.5699-0.05110.333.70724.272153.9355
360.43410.217-0.23240.2386-0.29410.41620.35680.16780.5017-0.13010.14350.2798-0.41360.00330.0260.4199-0.1655-0.03980.61520.00420.404737.305434.790154.3488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )A2 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 197 )A29 - 197
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 300 )A198 - 300
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 436 )A301 - 436
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 64 )B1 - 64
6X-RAY DIFFRACTION6chain 'B' and (resid 65 through 199 )B65 - 199
7X-RAY DIFFRACTION7chain 'B' and (resid 200 through 259 )B200 - 259
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 338 )B260 - 338
9X-RAY DIFFRACTION9chain 'B' and (resid 339 through 401 )B339 - 401
10X-RAY DIFFRACTION10chain 'B' and (resid 402 through 440 )B402 - 440
11X-RAY DIFFRACTION11chain 'F' and (resid 13 through 24 )F13 - 24
12X-RAY DIFFRACTION12chain 'F' and (resid 25 through 36 )F25 - 36
13X-RAY DIFFRACTION13chain 'F' and (resid 37 through 125 )F37 - 125
14X-RAY DIFFRACTION14chain 'F' and (resid 126 through 138 )F126 - 138
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 28 )C1 - 28
16X-RAY DIFFRACTION16chain 'C' and (resid 29 through 64 )C29 - 64
17X-RAY DIFFRACTION17chain 'C' and (resid 65 through 197 )C65 - 197
18X-RAY DIFFRACTION18chain 'C' and (resid 198 through 223 )C198 - 223
19X-RAY DIFFRACTION19chain 'C' and (resid 224 through 259 )C224 - 259
20X-RAY DIFFRACTION20chain 'C' and (resid 260 through 311 )C260 - 311
21X-RAY DIFFRACTION21chain 'C' and (resid 312 through 337 )C312 - 337
22X-RAY DIFFRACTION22chain 'C' and (resid 338 through 372 )C338 - 372
23X-RAY DIFFRACTION23chain 'C' and (resid 373 through 436 )C373 - 436
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 64 )D1 - 64
25X-RAY DIFFRACTION25chain 'D' and (resid 65 through 88 )D65 - 88
26X-RAY DIFFRACTION26chain 'D' and (resid 89 through 126 )D89 - 126
27X-RAY DIFFRACTION27chain 'D' and (resid 127 through 268 )D127 - 268
28X-RAY DIFFRACTION28chain 'D' and (resid 269 through 300 )D269 - 300
29X-RAY DIFFRACTION29chain 'D' and (resid 301 through 324 )D301 - 324
30X-RAY DIFFRACTION30chain 'D' and (resid 325 through 401 )D325 - 401
31X-RAY DIFFRACTION31chain 'D' and (resid 402 through 440 )D402 - 440
32X-RAY DIFFRACTION32chain 'E' and (resid 13 through 35 )E13 - 35
33X-RAY DIFFRACTION33chain 'E' and (resid 36 through 92 )E36 - 92
34X-RAY DIFFRACTION34chain 'E' and (resid 93 through 101 )E93 - 101
35X-RAY DIFFRACTION35chain 'E' and (resid 102 through 125 )E102 - 125
36X-RAY DIFFRACTION36chain 'E' and (resid 126 through 137 )E126 - 137

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