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- PDB-8jjc: Tubulin-Y62 -

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Basic information

Entry
Database: PDB / ID: 8jjc
TitleTubulin-Y62
Components
  • Stathmin-4
  • TTL
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / Microtubule
Function / homology
Function and homology information


Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / microtubule / neuron projection / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site ...Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsYang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Structure-based design and synthesis of BML284 derivatives: A novel class of colchicine-site noncovalent tubulin degradation agents.
Authors: Zhang, C. / Yan, W. / Liu, Y. / Tang, M. / Teng, Y. / Wang, F. / Hu, X. / Zhao, M. / Yang, J. / Li, Y.
History
DepositionMay 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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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 chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
F: TTL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,46225
Polymers262,9596
Non-polymers3,50319
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.493, 157.005, 180.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 50 or resid 52...
d_2ens_1(chain "C" and (resid 1 through 50 or resid 52...
d_1ens_2(chain "B" and (resid 2 through 38 or (resid 39...
d_2ens_2(chain "D" and (resid 2 through 161 or resid 163...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1METMETASNASNAA1 - 501 - 50
d_12ens_1PHEPHEPHEPHEAA52 - 6752 - 67
d_13ens_1ASPASPPHEPHEAA69 - 8769 - 87
d_14ens_1PROPROLEULEUAA89 - 11989 - 119
d_15ens_1ARGARGALAALAAA121 - 180121 - 180
d_16ens_1VALVALALAALAAA182 - 314182 - 314
d_17ens_1CYSCYSASPASPAA316 - 438316 - 438
d_18ens_1GTPGTPGTPGTPAG501
d_19ens_1MGMGMGMGAH502
d_21ens_1METMETASNASNCC1 - 501 - 50
d_22ens_1PHEPHEPHEPHECC52 - 6752 - 67
d_23ens_1ASPASPPHEPHECC69 - 8769 - 87
d_24ens_1PROPROLEULEUCC89 - 11989 - 119
d_25ens_1ARGARGALAALACC121 - 180121 - 180
d_26ens_1VALVALALAALACC182 - 314182 - 314
d_27ens_1CYSCYSASPASPCC316 - 438316 - 438
d_28ens_1GTPGTPGTPGTPCQ501
d_29ens_1MGMGMGMGCR502
d_11ens_2ARGARGASPASPBB2 - 1612 - 161
d_12ens_2ILEILESERSERBB163 - 275163 - 275
d_13ens_2LEULEUALAALABB284 - 438284 - 430
d_21ens_2ARGARGASPASPDD2 - 1612 - 161
d_22ens_2ILEILEALAALADD163 - 438163 - 430

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.945286255394, -0.254840184591, -0.20369186454), (0.281612559999, 0.952600596563, 0.115093307707), (0.164706591895, -0.166158309288, 0.972246447585)22.8742655775, -64.1364609998, -53.8593565915
2given(0.949131582542, -0.230835230175, -0.214159602939), (0.257604244864, 0.960359471985, 0.106535147234), (0.181078137965, -0.156284295686, 0.970971640612)22.2768354455, -63.8380246218, -54.6154367473

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 48299.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 22125.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#4: Protein TTL


Mass: 43825.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli)

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Non-polymers , 9 types, 35 molecules

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


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#9: Chemical ChemComp-UPO / 4-(6,7-dimethoxy-3,4-dihydro-1~{H}-isoquinolin-2-yl)-6-(3-methoxyphenyl)pyrimidin-2-amine


Mass: 392.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N4O3 / Feature type: SUBJECT OF INVESTIGATION
#10: 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
#11: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#12: 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
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 6% poly(ethylene glycol) 4000, 8% glycerol, 0.1 M MES (pH 6.7), 30 mM CaCl2, 30 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97777 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97777 Å / Relative weight: 1
ReflectionResolution: 2.76→93.73 Å / Num. obs: 1818003 / % possible obs: 99 % / Redundancy: 10.4 % / Biso Wilson estimate: 70.65 Å2 / CC1/2: 0.83 / Net I/σ(I): 7.62
Reflection shellResolution: 2.76→2.89 Å / Num. unique obs: 25474 / CC1/2: 0.12

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→47.74 Å / SU ML: 0.4122 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.774
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2643 1142 1.5 %
Rwork0.2353 75002 -
obs0.2357 76144 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.49 Å2
Refinement stepCycle: LAST / Resolution: 2.76→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17073 0 180 16 17269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003717691
X-RAY DIFFRACTIONf_angle_d0.679624058
X-RAY DIFFRACTIONf_chiral_restr0.04392654
X-RAY DIFFRACTIONf_plane_restr0.00443121
X-RAY DIFFRACTIONf_dihedral_angle_d19.36016422
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.50884597106
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.07412231329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.890.38321340.34158819X-RAY DIFFRACTION94.74
2.89-3.040.34281420.30369326X-RAY DIFFRACTION100
3.04-3.230.3321430.30369346X-RAY DIFFRACTION99.99
3.23-3.480.32041430.26989404X-RAY DIFFRACTION100
3.48-3.830.28291430.23839376X-RAY DIFFRACTION99.99
3.83-4.390.23991430.21229442X-RAY DIFFRACTION100
4.39-5.520.22591450.19739500X-RAY DIFFRACTION99.99
5.52-47.740.23111490.22319789X-RAY DIFFRACTION99.67

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