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- PDB-6zwb: Z-SBTub3 photoswitch bound to tubulin-DARPin D1 complex -

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Basic information

Entry
Database: PDB / ID: 6zwb
TitleZ-SBTub3 photoswitch bound to tubulin-DARPin D1 complex
Components
  • Designed Ankyrin Repeat Protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / photopharmacology / microtubule dynamics / cytoskeleton / tubulin polymerisation inhibitor / colchicine / antimitotic / azobenzene / cell division / spatiotemporal control
Function / homology
Function and homology information


positive regulation of axon guidance / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton ...positive regulation of axon guidance / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cilium / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / GTP binding / metal ion binding / cytoplasm / cytosol
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 / Chem-QRN / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.747 Å
AuthorsWranik, M. / Weinert, T. / Olieric, N. / Gao, L. / Kraus, Y.C.M. / Bingham, R. / Ntouliou, E. / Ahlfeld, J. / Thorn-Seshold, O. / Steinmetz, M.O. / Standfuss, J.
CitationJournal: Cell Chem Biol / Year: 2021
Title: A Robust, GFP-Orthogonal Photoswitchable Inhibitor Scaffold Extends Optical Control over the Microtubule Cytoskeleton.
Authors: Gao, L. / Meiring, J.C.M. / Kraus, Y. / Wranik, M. / Weinert, T. / Pritzl, S.D. / Bingham, R. / Ntouliou, E. / Jansen, K.I. / Olieric, N. / Standfuss, J. / Kapitein, L.C. / Lohmuller, T. / ...Authors: Gao, L. / Meiring, J.C.M. / Kraus, Y. / Wranik, M. / Weinert, T. / Pritzl, S.D. / Bingham, R. / Ntouliou, E. / Jansen, K.I. / Olieric, N. / Standfuss, J. / Kapitein, L.C. / Lohmuller, T. / Ahlfeld, J. / Akhmanova, A. / Steinmetz, M.O. / Thorn-Seshold, O.
History
DepositionJul 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)119,5497
Polymers118,2733
Non-polymers1,2764
Water11,980665
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-39 kcal/mol
Surface area36540 Å2
Unit cell
Length a, b, c (Å)73.869, 91.724, 83.006
Angle α, β, γ (deg.)90.000, 97.060, 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: synthetic construct (others)

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Non-polymers , 5 types, 669 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-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
#7: Chemical ChemComp-QRN / 5-[2-(1,3-benzothiazol-2-yl)ethyl]-2-methoxy-phenol


Mass: 285.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15NO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3000, ammonium sulfate, bis-tris methane

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2019
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.747→45.039 Å / Num. obs: 68165 / % possible obs: 61.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 23.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.054 / Rrim(I) all: 0.119 / Net I/σ(I): 9.2
Reflection shellResolution: 1.747→1.973 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3408 / CC1/2: 0.649 / Rpim(I) all: 0.424 / Rrim(I) all: 0.877 / % possible all: 10

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NM5

5nm5


Resolution: 1.747→45.039 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 2000 2.93 %
Rwork0.185 66146 -
obs0.1864 68146 61.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 371.86 Å2 / Biso mean: 44.3475 Å2 / Biso min: 7.84 Å2
Refinement stepCycle: final / Resolution: 1.747→45.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7873 0 113 665 8651
Biso mean--29.52 50.78 -
Num. residues----1023
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.747-1.79020.313830.33961232
1.7902-1.83860.1845160.28324906
1.8386-1.89280.3315250.298586011
1.8928-1.95380.3403410.2616134918
1.9538-2.02370.313610.2567200726
2.0237-2.10470.2849910.2479301039
2.1047-2.20050.30411520.2514503766
2.2005-2.31650.26672170.2469714393
2.3165-2.46160.26452320.2227678100
2.4616-2.65170.23352310.20667669100
2.6517-2.91850.24752330.20367706100
2.9185-3.34070.25422290.1834757398
3.3407-4.20840.19552340.14897733100
4.2084-45.0390.20032350.1451776899
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)
11.0492-0.49210.40831.40070.32381.36450.0985-0.0919-0.032-0.0007-0.0006-0.17750.12810.6384-0.02540.10580.0052-0.01160.2638-0.05090.1227124.724819.731111.2658
21.4487-0.1423-0.11570.7819-0.21381.51070.0027-0.115-0.02780.03130.0287-0.0151-0.1730.2167-0.0140.1422-0.05860.00370.0631-0.0410.072112.560628.354319.9385
31.26090.0899-0.26151.0459-0.08511.50680.0290.12810.04910.0287-0.0610.0839-0.13230.04220.01580.1868-0.0247-0.00330.1117-0.04720.116110.134226.09232.1352
41.1251-0.2958-0.63080.2140.24031.39480.06550.2807-0.1043-0.1025-0.06010.087-0.1465-0.0698-0.0060.1949-0.0243-0.01810.1206-0.02140.1201107.378227.6313-6.9047
50.97640.5406-0.7631.9303-1.12681.19890.1613-0.06050.1917-0.0128-0.0219-0.0007-0.3167-0.0245-0.06750.29530.0040.06510.0649-0.01840.166796.195740.997317.1799
62.0249-0.329-0.04641.0190.00561.0020.0584-0.8786-0.47480.3311-0.1258-0.4130.33410.3458-0.08010.04580.0858-0.09260.23810.17970.366892.77856.70946.2615
72.0664-0.1998-0.35050.8752-0.02180.93410.0241-0.34730.21490.0402-0.0363-0.1454-0.15150.17850.03640.1151-0.036-0.04450.18370.02150.178584.537419.716544.1611
81.1307-0.098-0.22951.4897-0.38191.2371-0.041-0.0036-0.3077-0.151-0.007-0.14660.14380.0260.03740.1130.00340.00110.11880.01680.205581.723911.430431.7229
92.13490.606-0.45530.3258-0.16183.3036-0.1480.4424-0.5945-0.11910.2407-0.16530.5498-0.2455-0.10110.2325-0.0572-0.0180.2811-0.05970.306875.19747.163122.4881
101.13990.1599-0.22121.0229-0.07331.0894-0.00230.4081-0.1866-0.2573-0.0249-0.14020.155-0.1782-0.00080.1599-0.00980.00660.161-0.03720.155979.63215.816123.1287
112.02510.2102-0.57690.625-0.71133.03470.3212-0.26140.55740.0728-0.1357-0.0572-0.51680.1445-0.04330.2363-0.02070.04980.1322-0.01870.284372.175429.90342.8026
122.6563-0.7798-0.83472.8390.4364.385-0.1432-0.20310.2793-0.00640.1056-0.2494-0.46930.6562-0.00390.2978-0.0202-0.05290.50320.01290.153455.345723.698570.3698
134.89460.2724-2.60931.73972.18674.5460.1939-0.1606-0.14910.7060.22960.23150.25020.38090.07630.57090.21840.09720.48620.14030.239952.125415.496373.5123
141.04330.0503-0.17852.05450.09861.4085-0.0656-0.17990.03390.1845-0.0383-0.1278-0.04820.2970.02130.14850.0094-0.01170.23390.01380.130351.775323.294463.7852
151.7669-0.0494-0.61022.14280.89273.3803-0.1383-0.3368-0.44520.1290.08070.11110.3966-0.09490.07110.23510.02210.06390.25190.14520.24446.660812.939664.1119
162.2416-0.4691-0.22461.037-0.02852.0482-0.026-0.2724-0.19090.11250.03510.09730.01270.028-0.01930.1055-0.00470.00140.16080.00590.089249.202219.336153.6749
171.1622-0.0153-0.06980.8116-0.02780.89870.05290.14830.03280.01690.02010.0714-0.1333-0.129-0.08350.11350.0046-0.02040.1701-0.00840.112850.719222.018545.4457
189.4016-0.0592-2.67770.77150.10983.4738-0.02750.0284-0.8848-0.13740.07530.05220.4804-0.053-0.02460.1817-0.0612-0.01140.1932-0.04510.226749.676410.71442.446
192.3071.724-1.19864.8884-1.90872.19420.05980.0178-0.0119-0.0721-0.17850.0201-0.2288-0.10650.09080.14810.0076-0.06660.23910.03170.085648.772924.47737.0425
202.9891-0.312-0.06710.48190.20480.7659-0.13440.1554-0.0154-0.48370.0683-0.1387-0.14490.17330.02910.2274-0.0128-0.02050.2513-0.02470.196557.592519.099632.3501
218.8751-0.57794.26332.05070.02532.09590.08930.4421-0.8381-0.42850.00060.38890.2964-0.2189-0.01550.2155-0.0227-0.01010.3016-0.05040.285853.362110.946832.5215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 72 )A1 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 197 )A73 - 197
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 273 )A198 - 273
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 401 )A274 - 401
5X-RAY DIFFRACTION5chain 'A' and (resid 402 through 437 )A402 - 437
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 127 )B1 - 127
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 199 )B128 - 199
8X-RAY DIFFRACTION8chain 'B' and (resid 200 through 273 )B200 - 273
9X-RAY DIFFRACTION9chain 'B' and (resid 274 through 311 )B274 - 311
10X-RAY DIFFRACTION10chain 'B' and (resid 312 through 401 )B312 - 401
11X-RAY DIFFRACTION11chain 'B' and (resid 402 through 441 )B402 - 441
12X-RAY DIFFRACTION12chain 'F' and (resid 13 through 24 )F13 - 24
13X-RAY DIFFRACTION13chain 'F' and (resid 25 through 35 )F25 - 35
14X-RAY DIFFRACTION14chain 'F' and (resid 36 through 59 )F36 - 59
15X-RAY DIFFRACTION15chain 'F' and (resid 60 through 69 )F60 - 69
16X-RAY DIFFRACTION16chain 'F' and (resid 70 through 101 )F70 - 101
17X-RAY DIFFRACTION17chain 'F' and (resid 102 through 125 )F102 - 125
18X-RAY DIFFRACTION18chain 'F' and (resid 126 through 134 )F126 - 134
19X-RAY DIFFRACTION19chain 'F' and (resid 135 through 148 )F135 - 148
20X-RAY DIFFRACTION20chain 'F' and (resid 149 through 158 )F149 - 158
21X-RAY DIFFRACTION21chain 'F' and (resid 159 through 167 )F159 - 167

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