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- PDB-7yz5: Molecular snapshots of drug release from tubulin: 100 millisecond... -

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Basic information

Entry
Database: PDB / ID: 7yz5
TitleMolecular snapshots of drug release from tubulin: 100 milliseconds (steady state)
Components
  • Designed Ankyrin Repeat Protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / time-resolved serial crystallography / tubulin dynamics / azobenzene dynamics
Function / homology
Function and homology information


positive regulation of axon guidance / microtubule-based process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / nervous system development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / protein heterodimerization activity ...positive regulation of axon guidance / microtubule-based process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / nervous system development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / protein heterodimerization activity / GTPase activity / GTP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsWranik, M. / Weinert, T. / Standfuss, J.
Funding support Switzerland, 6items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179351 Switzerland
Swiss National Science Foundation310030_197674 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
Swiss Nanoscience InstituteSNI #1904 Switzerland
Other governmentNCCR:MUST
Other governmentProject WA 1850/4-3
Citation
Journal: Nat Commun / Year: 2023
Title: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography.
Authors: Wranik, M. / Weinert, T. / Slavov, C. / Masini, T. / Furrer, A. / Gaillard, N. / Gioia, D. / Ferrarotti, M. / James, D. / Glover, H. / Carrillo, M. / Kekilli, D. / Stipp, R. / Skopintsev, P. ...Authors: Wranik, M. / Weinert, T. / Slavov, C. / Masini, T. / Furrer, A. / Gaillard, N. / Gioia, D. / Ferrarotti, M. / James, D. / Glover, H. / Carrillo, M. / Kekilli, D. / Stipp, R. / Skopintsev, P. / Brunle, S. / Muhlethaler, T. / Beale, J. / Gashi, D. / Nass, K. / Ozerov, D. / Johnson, P.J.M. / Cirelli, C. / Bacellar, C. / Braun, M. / Wang, M. / Dworkowski, F. / Milne, C. / Cavalli, A. / Wachtveitl, J. / Steinmetz, M.O. / Standfuss, J.
#1: Journal: Res Sq / Year: 2022
Title: Release of a photopharmacological drug from its protein target captured by time-resolved serial crystallography
Authors: Wranik, M. / Weinert, T. / Slavov, C. / Masini, T. / Furrer, A. / Gaillard, N. / Gioia, D. / Ferrarotti, M. / James, D. / Glover, H. / Carrillo, M. / Kekilli, D. / Stipp, R. / Skopintsev, P. ...Authors: Wranik, M. / Weinert, T. / Slavov, C. / Masini, T. / Furrer, A. / Gaillard, N. / Gioia, D. / Ferrarotti, M. / James, D. / Glover, H. / Carrillo, M. / Kekilli, D. / Stipp, R. / Skopintsev, P. / Brunle, S. / Muhlethaler, T. / Beale, J. / Gashi, D. / Nass, K. / Ozerov, D. / Johnson, P. / Cirelli, C. / Bacellar, C. / Braun, M. / Wang, M. / Dworkowski, F. / Milne, C. / Cavalli, A. / Wachtveitl, J. / Steinmetz, M. / Standfuss, J.
History
DepositionFeb 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
F: Designed Ankyrin Repeat Protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,3047
Polymers118,2733
Non-polymers1,0314
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-53 kcal/mol
Surface area36690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.280, 91.870, 83.690
Angle α, β, γ (deg.)90.000, 96.820, 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-2B chain


Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856
#3: Protein Designed Ankyrin Repeat Protein (DARPIN) D1


Mass: 18068.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 5 types, 154 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.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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.: 150 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium sulfate, 0.1M Bis/Tris-methane pH=5.5, 21% PEG 3000 (m/v)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→92.11 Å / Num. obs: 38945 / % possible obs: 60 % / Redundancy: 274.2 % / CC1/2: 0.992 / R split: 0.105 / Net I/σ(I): 7.87
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.25 / Num. unique obs: 117 / CC1/2: 0.528 / R split: 0.6948
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
CrystFEL0.9.1data reduction
CrystFEL0.9.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NQT

5nqt


Resolution: 2.11→73.75 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 2000 5.14 %
Rwork0.1728 36921 -
obs0.1757 38921 60.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.3 Å2 / Biso mean: 38.986 Å2 / Biso min: 8.61 Å2
Refinement stepCycle: final / Resolution: 2.11→73.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7913 0 62 150 8125
Biso mean--28.03 35.76 -
Num. residues----1023
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.160.18330.342265681
2.16-2.220.3805150.28832542696
2.22-2.280.3786240.303645648010
2.28-2.360.3147430.301478282518
2.36-2.440.3724590.2821100115925
2.44-2.540.3145850.27261596168136
2.54-2.660.26831270.25932341246854
2.66-2.80.34792180.24643955417391
2.8-2.970.30412340.229243814615100
2.97-3.20.25892350.207443634598100
3.2-3.520.2412390.183743764615100
3.52-4.030.19822370.142143774614100
4.03-5.080.18432380.123643994637100
5.08-73.750.18692430.14144764719100

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