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- PDB-8qlb: Ultrafast structural transitions in an azobenzene photoswitch at ... -

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Basic information

Entry
Database: PDB / ID: 8qlb
TitleUltrafast structural transitions in an azobenzene photoswitch at near-atomic resolution: 100 ns structure
Components
  • Designed Ankyrin Repeat Protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / Complex
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 / Azo-Combretastatin A4 (trans) / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWeinert, T. / Wranik, M. / Seidel, H.-P. / Church, J. / Steinmetz, M.O. / Schapiro, I. / Standfuss, J.
Funding support Switzerland, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation310030_197674 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
Swiss National Science FoundationCRSII5_213507 Switzerland
CitationJournal: To Be Published
Title: Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution
Authors: Weinert, T. / Wranik, M. / Seidel, H.-P. / Church, J. / Steinmetz, M.O. / Schapiro, I. / Standfuss, J.
History
DepositionSep 19, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionOct 2, 2024ID: 7YYX
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-54 kcal/mol
Surface area37510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.530, 92.580, 83.990
Angle α, β, γ (deg.)90.00, 96.71, 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 natural source / Source: (natural) Bos taurus (cattle) / Organ: brain / Tissue: brain / 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) / Organ: brain / Tissue: brain / 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 (E. coli)

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Non-polymers , 6 types, 344 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 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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 20, 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: 122150 / % possible obs: 100 % / Redundancy: 314.1 % / CC1/2: 0.964 / R split: 0.181 / Net I/σ(I): 4.05
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 0.62 / Num. unique obs: 12154 / CC1/2: 0.964 / R split: 1.804
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
CrystFEL0.9.0data reduction
CrystFEL0.9.0data scaling
PHENIX1.20_4459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→9.49 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2987 1966 1.93 %
Rwork0.2729 --
obs0.2734 101943 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→9.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7889 0 85 339 8313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.456
X-RAY DIFFRACTIONf_dihedral_angle_d15.0452993
X-RAY DIFFRACTIONf_chiral_restr0.0911235
X-RAY DIFFRACTIONf_plane_restr0.0081463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.38921380.40467098X-RAY DIFFRACTION98
1.85-1.90.42051410.38147148X-RAY DIFFRACTION99
1.9-1.950.43191420.37117226X-RAY DIFFRACTION99
1.95-2.020.39451420.35187164X-RAY DIFFRACTION99
2.02-2.090.38591420.33487135X-RAY DIFFRACTION99
2.09-2.170.35951400.31717141X-RAY DIFFRACTION99
2.17-2.270.37591400.30847190X-RAY DIFFRACTION99
2.27-2.390.3581410.30697133X-RAY DIFFRACTION99
2.39-2.530.30751410.29137149X-RAY DIFFRACTION99
2.53-2.720.32151370.28887112X-RAY DIFFRACTION98
2.72-2.990.32431400.27057146X-RAY DIFFRACTION98
2.99-3.40.27771390.2527106X-RAY DIFFRACTION98
3.4-4.230.23181400.23397128X-RAY DIFFRACTION98
4.23-9.490.27051430.24817101X-RAY DIFFRACTION97

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