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- PDB-7yz1: Molecular snapshots of drug release from tubulin: 1 millisecond a... -

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Basic information

Entry
Database: PDB / ID: 7yz1
TitleMolecular snapshots of drug release from tubulin: 1 millisecond after photoactivation.
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 / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / double-stranded RNA binding / nervous system development ...positive regulation of axon guidance / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / double-stranded RNA binding / nervous system development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / GTP binding / metal ion binding / cytosol / 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'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Azo-Combretastatin A4 (trans) / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 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 2.0Sep 13, 2023Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 3.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_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
F: Designed Ankyrin Repeat Protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6228
Polymers118,2733
Non-polymers1,3495
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-49 kcal/mol
Surface area37090 Å2
Unit cell
Length a, b, c (Å)74.530, 92.580, 83.990
Angle α, β, γ (deg.)90.000, 96.710, 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 (domestic 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 (domestic 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 , 6 types, 259 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: Chemical ChemComp-VYT / Azo-Combretastatin A4 (trans) / 2-methoxy-5-[(E)-(3,4,5-trimethoxyphenyl)diazenyl]phenol


Mass: 318.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N2O5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
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: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→11.09 Å / Num. obs: 122153 / % possible obs: 100 % / Redundancy: 328.9 % / CC1/2: 0.968 / R split: 0.181 / Net I/σ(I): 3.79
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 0.45 / Num. unique obs: 12154 / CC1/2: 0.217 / R split: 2.531
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: 2.2→9.49 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 39.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3517 1841 3.47 %
Rwork0.3018 51270 -
obs0.3036 53111 93.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.65 Å2 / Biso mean: 30.7067 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 2.2→9.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7892 0 85 254 8231
Biso mean--26.93 29.5 -
Num. residues----1018
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.4541650.3933750391591
2.26-2.320.4428970.38463856395391
2.32-2.40.47461860.38173827401392
2.4-2.480.4873750.3793663373886
2.48-2.580.41651850.34233864404993
2.58-2.690.3927850.34883790387589
2.69-2.830.38741870.31353930411794
2.83-3.010.3456940.30874078417295
3.01-3.230.36211850.30484006419196
3.23-3.540.365970.29054109420696
3.54-4.020.33791940.26844066426097
4.02-4.940.2331980.24864202430098
4.94-9.490.3021930.27754129432297

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