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- PDB-7cbz: Crystal structure of T2R-TTL-A31 complex -

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Basic information

Entry
Database: PDB / ID: 7cbz
TitleCrystal structure of T2R-TTL-A31 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 / 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 ...tubulin-tyrosine ligase activity / 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 / microtubule depolymerization / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / growth cone / microtubule / neuron projection / nucleotide binding / 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. / Stathmin-like (SLD) domain profile. ...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
Chem-FUO / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesSus scrofa (pig)
Rattus norvegicus (Norway rat)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsYang, J.H. / Yan, W.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Design, Synthesis, and Bioactivity Evaluation of Dual-Target Inhibitors of Tubulin and Src Kinase Guided by Crystal Structure.
Authors: Wang, L. / Zheng, Y. / Li, D. / Yang, J. / Lei, L. / Yan, W. / Zheng, W. / Tang, M. / Shi, M. / Zhang, R. / Cai, X. / Ni, H. / Ma, X. / Li, N. / Hong, F. / Ye, H. / Chen, L.
History
DepositionJun 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)270,29024
Polymers266,7746
Non-polymers3,51518
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: No
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.805, 156.630, 181.469
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-ID
d_1ens_1
d_2ens_2
/ NCS ensembles :
ID
ens_2
ens_1

NCS oper:
IDCodeMatrixVector
1given(0.940057174247, -0.268999421515, -0.209599189818), (0.298546015482, 0.946226923379, 0.124598900925), (0.164811364254, -0.179705093686, 0.969816113248)24.2437874465, -64.3798154358, -52.9877206706
2given(0.946059255663, -0.240533684054, -0.217060893782), (0.270495631434, 0.95514797098, 0.120517496275), (0.178336754903, -0.172730716343, 0.968689889223)23.0022023415, -64.099170951, -53.5749774

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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 genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBA1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49999.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / 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: 44240.352 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 , 7 types, 134 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-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-FUO / 2-[5-[4-[2-[4-(2-cyclopropylethanoyl)piperazin-1-yl]ethoxy]phenyl]pyridin-2-yl]-N-(phenylmethyl)ethanamide


Mass: 512.643 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H36N4O3 / Feature type: SUBJECT OF INVESTIGATION
#9: 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
#10: 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
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 56.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6% PEG4000, 8% glycerol, 0.1 M MES (pH 6.7), 30 mM CaCl2, and 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: 0.97852 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: 2.61→19.81 Å / Num. obs: 89791 / % possible obs: 98.01 % / Redundancy: 7.1 % / Biso Wilson estimate: 58.36 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.3
Reflection shellResolution: 2.61→2.7 Å / Num. unique obs: 7278 / CC1/2: 0.665

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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: 6KNZ

6knz


Resolution: 2.61→19.76 Å / SU ML: 0.3758 / Cross valid method: FREE R-VALUE / σ(F): 1.65 / Phase error: 28.9015
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2547 4262 5.01 %
Rwork0.2062 80758 -
obs0.2086 85020 92.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.7 Å2
Refinement stepCycle: LAST / Resolution: 2.61→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17073 0 219 116 17408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006917726
X-RAY DIFFRACTIONf_angle_d0.873824040
X-RAY DIFFRACTIONf_chiral_restr0.05442621
X-RAY DIFFRACTIONf_plane_restr0.00513120
X-RAY DIFFRACTIONf_dihedral_angle_d21.04416601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.640.372910.35831674X-RAY DIFFRACTION58.23
2.64-2.670.32821350.32022427X-RAY DIFFRACTION84.69
2.67-2.70.36931470.29642763X-RAY DIFFRACTION96.04
2.7-2.730.31391370.28062796X-RAY DIFFRACTION98.56
2.73-2.770.3241210.28852874X-RAY DIFFRACTION98.68
2.77-2.810.38981470.27982817X-RAY DIFFRACTION98.44
2.81-2.850.32411320.26652841X-RAY DIFFRACTION97.89
2.85-2.890.31711570.2682773X-RAY DIFFRACTION97.99
2.89-2.930.34771370.26392811X-RAY DIFFRACTION97.55
2.93-2.980.32611510.25972805X-RAY DIFFRACTION97.62
2.98-3.030.32751430.26142809X-RAY DIFFRACTION97.2
3.03-3.090.31911320.24382805X-RAY DIFFRACTION96.33
3.09-3.150.28641350.24682792X-RAY DIFFRACTION96.7
3.15-3.210.33481650.24742712X-RAY DIFFRACTION96.61
3.21-3.280.29521440.24542817X-RAY DIFFRACTION96.36
3.28-3.360.28081570.232763X-RAY DIFFRACTION96.37
3.36-3.440.28821460.22662759X-RAY DIFFRACTION96.1
3.44-3.530.28621590.22212735X-RAY DIFFRACTION95.51
3.53-3.640.26951440.20832757X-RAY DIFFRACTION94.5
3.64-3.750.2691580.19112706X-RAY DIFFRACTION94.52
3.75-3.890.26691600.19052714X-RAY DIFFRACTION94.26
3.89-4.040.20891300.18212729X-RAY DIFFRACTION93.13
4.04-4.220.25311330.17592709X-RAY DIFFRACTION93.3
4.22-4.440.20461490.16682703X-RAY DIFFRACTION92.81
4.44-4.720.19661560.15382669X-RAY DIFFRACTION92.26
4.72-5.080.20551590.16132635X-RAY DIFFRACTION90.86
5.08-5.580.23791470.19272642X-RAY DIFFRACTION89.82
5.58-6.360.25371300.21652642X-RAY DIFFRACTION88.93
6.36-7.930.2071300.19882594X-RAY DIFFRACTION86.56
7.93-19.760.1741300.1652485X-RAY DIFFRACTION80.26

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