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- PDB-8cld: Ansamitocin P3 bound to tubulin (T2R-TTL) complex -

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Basic information

Entry
Database: PDB / ID: 8cld
TitleAnsamitocin P3 bound to tubulin (T2R-TTL) complex
Components
  • Detyrosinated tubulin alpha-1B chain
  • Stathmin-4
  • Tubulin beta-2B chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / Drug-tubulin-complex Cell cycle inhibition
Function / homology
Function and homology information


tubulin-tyrosine ligase / tubulin-tyrosine ligase activity / positive regulation of axon guidance / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / spindle microtubule / protein modification process / structural constituent of cytoskeleton ...tubulin-tyrosine ligase / tubulin-tyrosine ligase activity / positive regulation of axon guidance / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / growth cone / 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 / Golgi apparatus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. ...: / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-BKF / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin--tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Pavo cristatus (Indian peafowl)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWranik, M. / Kepa, M.W. / Bertrand, Q. / Weinert, T. / Steinmetz, M. / Standfuss, J.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179351 Switzerland
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers.
Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / ...Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / Ozerov, D. / Cirelli, C. / Johnson, P.J.M. / Dworkowski, F. / Beale, J.H. / Stubbs, S. / Zamofing, T. / Schneider, M. / Krauskopf, K. / Gao, L. / Thorn-Seshold, O. / Bostedt, C. / Bacellar, C. / Steinmetz, M.O. / Milne, C. / Standfuss, J.
History
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Detyrosinated tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Detyrosinated tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,13917
Polymers266,9126
Non-polymers3,22611
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21290 Å2
ΔGint-116 kcal/mol
Surface area80890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.060, 159.610, 180.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Detyrosinated tubulin alpha-1B chain


Mass: 50204.445 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856
#3: Protein Stathmin-4


Mass: 22125.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63042
#4: Protein Tubulin tyrosine ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pavo cristatus (Indian peafowl) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8C9FGJ1

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Non-polymers , 7 types, 14 molecules

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


Mass: 523.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-BKF / (1S,2S,3S,5S,6S,16Z,18Z,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl 2-methylpropanoate


Mass: 635.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H43ClN2O9 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5
Details: 6% PEG4000 (w/v), 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

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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: 1.03 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3.1→15.17 Å / Num. obs: 56426 / % possible obs: 100 % / Redundancy: 38.5 % / CC1/2: 0.776 / Net I/σ(I): 3.38
Reflection shellResolution: 3.1→3.2 Å / Mean I/σ(I) obs: 1.25 / Num. unique obs: 5544 / CC1/2: 0.42
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: Hydroxyethylcellulose / Description: High-viscosity injection / Injector diameter: 75 µm

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Processing

Software
NameVersionClassification
PHENIX1.20_4487refinement
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
PHENIX1.20_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→15.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2412 --
Rwork0.1996 --
obs0.2005 50716 99.93 %
Refinement stepCycle: LAST / Resolution: 3.2→15.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17284 0 200 3 17487

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