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- PDB-7emj: Crystal structure of T2R-TTL-Barbigerone complex -

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Basic information

Entry
Database: PDB / ID: 7emj
TitleCrystal structure of T2R-TTL-Barbigerone complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE/INHIBITOR / Tubulin / Cancer / CELL CYCLE-INHIBITOR complex
Function / homology
Function and homology information


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 ...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 / microtubule depolymerization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / 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 / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / 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 / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #11480 / 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. ...Rossmann fold - #11480 / 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/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-J6L / 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: 2.33 Å
AuthorsYang, J.H. / Yan, W.
CitationJournal: Phytomedicine / Year: 2023
Title: Crystal structure of tubulin-barbigerone complex enables rational design of potent anticancer agents with isoflavone skeleton.
Authors: Yan, W. / Li, Y. / Liu, Y. / Wen, Y. / Pei, H. / Yang, J. / Chen, L.
History
DepositionApr 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: Tubulin tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,19824
Polymers266,7286
Non-polymers3,47018
Water14,268792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22850 Å2
ΔGint-170 kcal/mol
Surface area79910 Å2
Unit cell
Length a, b, c (Å)105.030, 157.252, 180.606
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

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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: 49907.770 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 Tubulin tyrosine ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

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Non-polymers , 8 types, 810 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-J6L / 8,8-dimethyl-3-(2,4,5-trimethoxyphenyl)pyrano[2,3-f]chromen-4-one


Mass: 394.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22O6 / 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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6% PEG 4000, 5% glycerol, 0.1 M MES, 30 mM CaCl2 and 30 mM MgCl2, pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 126418 / % possible obs: 99.18 % / Redundancy: 11.5 % / Biso Wilson estimate: 27.83 Å2 / CC1/2: 0.993 / Net I/σ(I): 24
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 6262 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NKZ

6nkz


Resolution: 2.33→46.9 Å / SU ML: 0.241 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2411 6360 5.03 %
Rwork0.1976 120058 -
obs0.1998 126418 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.93 Å2
Refinement stepCycle: LAST / Resolution: 2.33→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17386 0 207 792 18385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009118073
X-RAY DIFFRACTIONf_angle_d1.218424528
X-RAY DIFFRACTIONf_chiral_restr0.06062667
X-RAY DIFFRACTIONf_plane_restr0.00833182
X-RAY DIFFRACTIONf_dihedral_angle_d15.52952515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.360.31111610.24183140X-RAY DIFFRACTION78.73
2.36-2.390.27851980.22924012X-RAY DIFFRACTION99.67
2.39-2.420.28591930.21933978X-RAY DIFFRACTION99.71
2.42-2.450.25982060.20893991X-RAY DIFFRACTION99.79
2.45-2.480.24272190.21413963X-RAY DIFFRACTION99.88
2.48-2.510.27372340.21533967X-RAY DIFFRACTION99.9
2.51-2.550.2762160.21574016X-RAY DIFFRACTION99.91
2.55-2.590.26151910.21544014X-RAY DIFFRACTION99.98
2.59-2.630.24792290.21493982X-RAY DIFFRACTION99.98
2.63-2.670.28811940.21413992X-RAY DIFFRACTION99.95
2.67-2.720.27252130.2224018X-RAY DIFFRACTION99.95
2.72-2.770.26382190.2233972X-RAY DIFFRACTION99.98
2.77-2.820.2632320.22474018X-RAY DIFFRACTION100
2.82-2.880.28072110.21333975X-RAY DIFFRACTION99.98
2.88-2.940.26392050.21584009X-RAY DIFFRACTION99.95
2.94-3.010.2552190.21054042X-RAY DIFFRACTION100
3.01-3.080.26182090.20934014X-RAY DIFFRACTION100
3.08-3.170.26572110.20894010X-RAY DIFFRACTION100
3.17-3.260.26462120.21834022X-RAY DIFFRACTION99.98
3.26-3.370.26092380.20894000X-RAY DIFFRACTION99.95
3.37-3.490.25022150.19624043X-RAY DIFFRACTION99.98
3.49-3.630.2232310.18924022X-RAY DIFFRACTION99.98
3.63-3.790.21261890.18274054X-RAY DIFFRACTION99.95
3.79-3.990.22112170.17364038X-RAY DIFFRACTION99.95
3.99-4.240.20812140.16354065X-RAY DIFFRACTION99.98
4.24-4.570.18352090.15064065X-RAY DIFFRACTION99.93
4.57-5.030.19092180.15124095X-RAY DIFFRACTION99.93
5.03-5.750.21692190.18834091X-RAY DIFFRACTION99.93
5.75-7.240.24862140.2214166X-RAY DIFFRACTION99.95
7.24-46.90.24632240.21634284X-RAY DIFFRACTION99.08
Refinement TLS params.Method: refined / Origin x: 17.3289388727 Å / Origin y: 44.0915699251 Å / Origin z: 26.980844301 Å
111213212223313233
T0.0912810532126 Å20.00508400661286 Å20.00891226095335 Å2-0.159555630199 Å2-0.00528262217508 Å2--0.196593232334 Å2
L0.1064276818 °2-0.0180011644605 °2-0.0591330883494 °2-0.521639637421 °20.552181457049 °2--0.918449779864 °2
S-0.0257533385124 Å °-0.00191989584566 Å °0.00652829356659 Å °0.0398134732078 Å °0.0528717912958 Å °0.0012095543749 Å °0.0306328915053 Å °0.0424115787212 Å °-0.017868863532 Å °
Refinement TLS groupSelection details: all

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