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- PDB-9ixb: Structure of tubulin and nitrogen-containing heterocyclic substit... -

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Basic information

Entry
Database: PDB / ID: 9ixb
TitleStructure of tubulin and nitrogen-containing heterocyclic substituted podophyllotoxin derivatives complex
Components
  • Detyrosinated tubulin alpha-1B chain
  • Stathmin-4
  • Tubulin beta chain
  • Tubulin--tyrosine ligase
KeywordsCELL CYCLE / tublin / GTP / inhibitor / two binding sites
Function / homology
Function and homology information


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 ...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 / microtubule depolymerization / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / 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 / 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
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 / IMIDAZOLE / 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: 3.48 Å
AuthorsBi, J. / Zhao, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of tubulin and nitrogen-containing heterocyclic substituted podophyllotoxin derivatives complex
Authors: Bi, J.
History
DepositionJul 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: 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)258,08920
Polymers254,6596
Non-polymers3,43014
Water25214
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)104.597, 155.892, 181.504
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 2 through 50 or resid 52...
d_2ens_1(chain "C" and (resid 2 through 32 or (resid 33...
d_1ens_2(chain "B" and (resid 2 through 15 or resid 17...
d_2ens_2(chain "D" and (resid 2 through 15 or (resid 17...

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_1ARGARGASNASNAA2 - 502 - 50
d_12ens_1PHEPHEALAALAAA52 - 6552 - 65
d_13ens_1PHEPHEPHEPHEAA6767
d_14ens_1ASPASPARGARGAA69 - 7969 - 79
d_15ens_1GLYGLYPHEPHEAA81 - 13581 - 135
d_16ens_1VALVALTHRTHRAA137 - 150137 - 150
d_17ens_1LEULEUTHRTHRAA152 - 193152 - 193
d_18ens_1LEULEUALAALAAA195 - 208195 - 208
d_19ens_1TYRTYRTYRTYRAA210210
d_110ens_1ILEILEASPASPAA212 - 245212 - 245
d_111ens_1ALAALAALAALAAA247 - 314247 - 314
d_112ens_1LEULEUILEILEAA317 - 355317 - 355
d_113ens_1TYRTYRASPASPAA357 - 438357 - 438
d_114ens_1GTPGTPGTPGTPAG501
d_21ens_1ARGARGASNASNCC2 - 502 - 50
d_22ens_1PHEPHEALAALACC52 - 6552 - 65
d_23ens_1PHEPHEPHEPHECC6767
d_24ens_1ASPASPARGARGCC69 - 7969 - 79
d_25ens_1GLYGLYPHEPHECC81 - 13581 - 135
d_26ens_1VALVALTHRTHRCC137 - 150137 - 150
d_27ens_1LEULEUTHRTHRCC152 - 193152 - 193
d_28ens_1LEULEUALAALACC195 - 208195 - 208
d_29ens_1TYRTYRTYRTYRCC210210
d_210ens_1ILEILEALAALACC212 - 314212 - 314
d_211ens_1LEULEUILEILECC317 - 355317 - 355
d_212ens_1TYRTYRASPASPCC357 - 438357 - 438
d_213ens_1GTPGTPGTPGTPCP501
d_11ens_2ARGARGGLNGLNBB2 - 152 - 15
d_12ens_2GLYGLYILEILEBB17 - 4917 - 47
d_13ens_2VALVALLEULEUBB51 - 13749 - 135
d_14ens_2HISHISGLYGLYBB139 - 146137 - 144
d_15ens_2GLYGLYILEILEBB148 - 154146 - 152
d_16ens_2LYSLYSTHRTHRBB156 - 220154 - 218
d_17ens_2PROPROPROPROBB222 - 245220 - 243
d_18ens_2GLNGLNPHEPHEBB247 - 268245 - 266
d_19ens_2PROPROLEULEUBB270 - 275268 - 273
d_110ens_2GLNGLNALAALABB282 - 383280 - 373
d_111ens_2GLNGLNMETMETBB385 - 413375 - 403
d_112ens_2GLUGLUGLUGLUBB415 - 422405 - 412
d_113ens_2ASNASNASPASPBB424 - 437414 - 427
d_21ens_2ARGARGGLNGLNDD2 - 152 - 15
d_22ens_2GLYGLYILEILEDD17 - 4917 - 47
d_23ens_2VALVALGLUGLUDD51 - 5549 - 53
d_24ens_2GLYGLYLEULEUDD58 - 13756 - 135
d_25ens_2HISHISGLYGLYDD139 - 146137 - 144
d_26ens_2GLYGLYILEILEDD148 - 154146 - 152
d_27ens_2LYSLYSTHRTHRDD156 - 220154 - 218
d_28ens_2PROPROPHEPHEDD222 - 268220 - 266
d_29ens_2PROPROLEULEUDD270 - 275268 - 273
d_210ens_2GLNGLNALAALADD282 - 383280 - 373
d_211ens_2GLNGLNMETMETDD385 - 413375 - 403
d_212ens_2GLUGLUGLUGLUDD415 - 422405 - 412
d_213ens_2ASNASNASPASPDD424 - 437414 - 427

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.943820808091, -0.259844151329, 0.204164882473), (0.287153443474, 0.950642732533, -0.117564003773), (-0.163539542975, 0.169586002082, 0.971851534845)-23.4064666469, 64.1243740125, -54.3269354736
2given(0.947165209769, -0.233844832128, 0.219532821896), (0.263793129401, 0.957280594122, -0.118435843388), (-0.182458900258, 0.170089560541, 0.968389534801)-22.6403729665, 64.3112669708, -54.4450324417

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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: 48306.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480UE93
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16326.670 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: 43786.852 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) / References: tubulin-tyrosine ligase

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Non-polymers , 11 types, 28 molecules

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


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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-A1ECQ / (5~{S},5~{a}~{S},8~{a}~{R},9~{R})-5-(1~{H}-indazol-5-ylamino)-9-(3,4,5-trimethoxyphenyl)-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[6,5-f][1,3]benzodioxol-8-one


Mass: 529.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C29H27N3O7 / Feature type: SUBJECT OF INVESTIGATION
#12: 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
#13: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#14: 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
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 6% PEG4000, 6% glycerol, 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: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.48→25.98 Å / Num. obs: 37680 / % possible obs: 97.16 % / Redundancy: 1.9 % / Biso Wilson estimate: 91.24 Å2 / Rmerge(I) obs: 0.05343 / Rpim(I) all: 0.05343 / Rrim(I) all: 0.07556 / Net I/σ(I): 13.22
Reflection shellResolution: 3.48→3.604 Å / Num. unique obs: 3783 / CC1/2: 0.837 / CC star: 0.955

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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: 3.48→25.98 Å / SU ML: 0.4499 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2666 1873 4.97 %
Rwork0.2216 35803 -
obs0.2238 37676 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.45 Å2
Refinement stepCycle: LAST / Resolution: 3.48→25.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15546 0 160 14 15720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011816208
X-RAY DIFFRACTIONf_angle_d1.451922204
X-RAY DIFFRACTIONf_chiral_restr0.07692551
X-RAY DIFFRACTIONf_plane_restr0.0112875
X-RAY DIFFRACTIONf_dihedral_angle_d11.66175520
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.3715787892
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.896554151418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.48-3.570.40121490.28692773X-RAY DIFFRACTION99.97
3.57-3.680.27971510.25342781X-RAY DIFFRACTION100
3.68-3.80.29341680.23992759X-RAY DIFFRACTION100
3.8-3.930.2814960.23421840X-RAY DIFFRACTION66.53
3.93-4.090.29581520.21692801X-RAY DIFFRACTION100
4.09-4.270.26441530.21212801X-RAY DIFFRACTION99.97
4.27-4.50.27281470.2012800X-RAY DIFFRACTION99.93
4.5-4.780.24981460.18492814X-RAY DIFFRACTION100
4.78-5.150.23881290.20042836X-RAY DIFFRACTION100
5.15-5.660.28271530.23662836X-RAY DIFFRACTION100
5.66-6.470.30741260.25922885X-RAY DIFFRACTION100
6.47-8.110.26281410.23082881X-RAY DIFFRACTION99.97
8.11-25.980.21861620.20732996X-RAY DIFFRACTION99.91
Refinement TLS params.Method: refined / Origin x: -17.5858371282 Å / Origin y: -43.3948686644 Å / Origin z: 24.483380202 Å
111213212223313233
T0.381070590586 Å20.0230165377431 Å2-0.00656037868738 Å2-0.506345582533 Å2-0.00157811568379 Å2--0.544467593373 Å2
L0.294831338499 °2-0.0396447473758 °20.129971564329 °2-0.75319320727 °2-0.640435359693 °2--1.16921655934 °2
S-0.0495578480043 Å °-0.00848381695061 Å °-0.0286220266913 Å °0.0567574970506 Å °0.0683514958349 Å °-0.0435220533441 Å °-0.0234122169907 Å °-0.0271769706665 Å °-0.0172762677671 Å °
Refinement TLS groupSelection details: all

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