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- PDB-8wmo: Crystal structure analysis of tubulin and heterocyclic podophyllo... -

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Basic information

Entry
Database: PDB / ID: 8wmo
TitleCrystal structure analysis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents
Components
  • Detyrosinated tubulin alpha-1B chain
  • Stathmin-4
  • Tubulin beta chain
  • Tubulin--tyrosine ligase
KeywordsCELL CYCLE / tubulin / heterocyclic podophyllotoxins complex / anticancer agents
Function / homology
Function and homology information


tubulin-tyrosine ligase / tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin ...tubulin-tyrosine ligase / tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / microtubule depolymerization / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
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. / 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 / DI(HYDROXYETHYL)ETHER / : / Tubulin--tyrosine ligase / 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: 2.89 Å
AuthorsZhao, W. / Bi, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0905700 China
CitationJournal: To Be Published
Title: Crystal structure analysis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents
Authors: Zhao, W.
History
DepositionOct 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 9, 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: Detyrosinated tubulin alpha-1B chain
B: Tubulin beta chain
C: Detyrosinated tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
F: Tubulin--tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,14127
Polymers258,1796
Non-polymers3,96221
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.820, 156.446, 179.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 72 or (resid 73...
d_2ens_1(chain "C" and ((resid 1 through 2 and (name N...
d_1ens_2(chain "B" and (resid 1 through 45 or (resid 46...
d_2ens_2(chain "D" and (resid 1 through 36 or (resid 37...

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_1METMETVALVALAA1 - 4371 - 437
d_12ens_1EDOEDOEDOEDOAI503
d_21ens_1METMETTYRTYRCC1 - 2721 - 272
d_22ens_1PROPROGLUGLUCC274 - 279274 - 279
d_23ens_1HISHISVALVALCC283 - 437283 - 437
d_24ens_1EDOEDOEDOEDOCU506
d_11ens_2METMETALAALABB1 - 541 - 54
d_12ens_2ASNASNLEULEUBB57 - 27357 - 273
d_13ens_2LEULEUALAALABB284 - 428284 - 428
d_14ens_2EDOEDOEDOEDOBO505
d_21ens_2METMETALAALADD1 - 4281 - 428
d_22ens_2EDOEDOEDOEDODZ504

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.948220911024, 0.250240869836, -0.195592972675), (-0.274348198834, 0.955612548112, -0.107413796538), (0.160031777133, 0.155512587767, 0.974784932872)-22.1075737382, -63.7603487608, 54.6035280217
2given(0.94769577665, 0.231582990508, -0.219640691649), (-0.257937248942, 0.961006053498, -0.0996781859197), (0.187992261886, 0.15111811158, 0.970475257708)-22.4690859897, -63.5053446374, 55.2670747663

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Detyrosinated tubulin alpha-1B chain


Mass: 48966.324 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


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1UIR5
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16282.527 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 Tubulin--tyrosine ligase


Mass: 43964.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for source organism Gallus gallus is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A8C9FGJ1.
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8C9FGJ1, tubulin-tyrosine ligase

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Non-polymers , 10 types, 52 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.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: 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
#10: 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
#11: Chemical ChemComp-WIW / (5~{S},5~{a}~{R},8~{a}~{R},9~{R})-5-pyrimidin-2-ylsulfanyl-9-(3,4,5-trimethoxyphenyl)-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[5,6-f][1,3]benzodioxol-8-one


Mass: 508.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H24N2O7S / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#13: 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
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 6% glycerol, 6% PEG4000, 30 mM MgCl2, 30 mM CaCl2, 100 mM MES-Na

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 65706 / % possible obs: 99.56 % / Redundancy: 6.7 % / Biso Wilson estimate: 71.89 Å2 / CC1/2: 0.85 / Net I/σ(I): 71.89
Reflection shellResolution: 2.893→2.996 Å / Num. unique obs: 6356 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→49.86 Å / SU ML: 0.4094 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2662 3224 4.91 %
Rwork0.2239 62433 -
obs0.2259 65657 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.9 Å2
Refinement stepCycle: LAST / Resolution: 2.89→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16429 0 247 31 16707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010717031
X-RAY DIFFRACTIONf_angle_d1.275723179
X-RAY DIFFRACTIONf_chiral_restr0.06332587
X-RAY DIFFRACTIONf_plane_restr0.01013005
X-RAY DIFFRACTIONf_dihedral_angle_d19.53476009
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.70545076343
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.17184004205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.940.34841380.31022544X-RAY DIFFRACTION95.38
2.94-2.980.33111460.28282699X-RAY DIFFRACTION99.89
2.98-3.030.32631360.27552672X-RAY DIFFRACTION100
3.03-3.080.34981310.27912714X-RAY DIFFRACTION99.89
3.08-3.140.33711340.28092690X-RAY DIFFRACTION99.79
3.14-3.20.37251360.2842688X-RAY DIFFRACTION99.89
3.2-3.260.30531340.27222714X-RAY DIFFRACTION99.96
3.26-3.340.34991450.27782672X-RAY DIFFRACTION99.96
3.34-3.410.30051310.27522711X-RAY DIFFRACTION100
3.41-3.50.29051480.25262686X-RAY DIFFRACTION99.86
3.5-3.590.27191440.23892708X-RAY DIFFRACTION100
3.59-3.70.27811250.23162713X-RAY DIFFRACTION100
3.7-3.820.28711530.22672708X-RAY DIFFRACTION99.69
3.82-3.950.25981370.21982681X-RAY DIFFRACTION99.96
3.95-4.110.25281390.21442719X-RAY DIFFRACTION99.79
4.11-4.30.27041370.20922733X-RAY DIFFRACTION99.97
4.3-4.530.22691400.18792728X-RAY DIFFRACTION99.93
4.53-4.810.21921270.18892750X-RAY DIFFRACTION99.83
4.81-5.180.22531260.19732769X-RAY DIFFRACTION99.97
5.18-5.70.25531450.21632736X-RAY DIFFRACTION99.9
5.7-6.520.25481470.23432767X-RAY DIFFRACTION99.69
6.52-8.210.23821710.21642775X-RAY DIFFRACTION99.93
8.22-49.860.24741540.19382856X-RAY DIFFRACTION97.57

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