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- PDB-6nng: Tubulin-RB3_SLD-TTL in complex with compound DJ95 -

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Basic information

Entry
Database: PDB / ID: 6nng
TitleTubulin-RB3_SLD-TTL in complex with compound DJ95
Components
  • Stathmin-4
  • Tubulin Tyrosine Ligase
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / Microtubule Inhibitor / Colchicine / Cancer
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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 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. / 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 / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-DJ9 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin tyrosine ligase / Tubulin beta chain / Tubulin alpha-1B chain / Stathmin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 Å
AuthorsKumar, G. / Wang, Y. / Li, W. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA148706 United States
CitationJournal: Mol.Pharmacol. / Year: 2019
Title: Colchicine Binding Site Agent DJ95 Overcomes Drug Resistance and Exhibits Antitumor Efficacy.
Authors: Arnst, K.E. / Wang, Y. / Lei, Z.N. / Hwang, D.J. / Kumar, G. / Ma, D. / Parke, D.N. / Chen, Q. / Yang, J. / White, S.W. / Seagroves, T.N. / Chen, Z.S. / Miller, D.D. / Li, W.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,79120
Polymers261,3056
Non-polymers3,48614
Water10,269570
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.418, 157.979, 182.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 2 through 18 or (resid 19...
21(chain D and (resid 2 through 36 or (resid 37...
12(chain A and ((resid 1 and (name N or name...
22(chain C and (resid 1 through 111 or (resid 112...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resid 2 through 18 or (resid 19...B2 - 18
121(chain B and (resid 2 through 18 or (resid 19...B19
131(chain B and (resid 2 through 18 or (resid 19...B2 - 502
141(chain B and (resid 2 through 18 or (resid 19...B2 - 502
151(chain B and (resid 2 through 18 or (resid 19...B2 - 502
161(chain B and (resid 2 through 18 or (resid 19...B2 - 502
211(chain D and (resid 2 through 36 or (resid 37...D2 - 36
221(chain D and (resid 2 through 36 or (resid 37...D37
231(chain D and (resid 2 through 36 or (resid 37...D1 - 431
241(chain D and (resid 2 through 36 or (resid 37...D1 - 431
251(chain D and (resid 2 through 36 or (resid 37...D1 - 431
112(chain A and ((resid 1 and (name N or name...A1
122(chain A and ((resid 1 and (name N or name...A1 - 502
132(chain A and ((resid 1 and (name N or name...A1 - 502
142(chain A and ((resid 1 and (name N or name...A1 - 502
152(chain A and ((resid 1 and (name N or name...A1 - 502
212(chain C and (resid 1 through 111 or (resid 112...C1 - 111
222(chain C and (resid 1 through 111 or (resid 112...C112
232(chain C and (resid 1 through 111 or (resid 112...C1 - 502
242(chain C and (resid 1 through 111 or (resid 112...C1 - 502
252(chain C and (resid 1 through 111 or (resid 112...C1 - 502
262(chain C and (resid 1 through 111 or (resid 112...C1 - 502

NCS ensembles :
ID
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: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7, UniProt: P02554*PLUS
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STMN4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H169
#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, 584 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-CA / CALCIUM ION


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


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-DJ9 / 2-(1H-indol-6-yl)-4-(3,4,5-trimethoxyphenyl)-1H-imidazo[4,5-c]pyridine


Mass: 400.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20N4O3 / Feature type: SUBJECT OF INVESTIGATION
#11: 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
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O

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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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG 4000, 5% Glycerol, 0.1 M MES, 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: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.397→50 Å / Num. obs: 120100 / % possible obs: 99.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 35.71 Å2 / Net I/σ(I): 20.89
Reflection shellResolution: 2.397→2.44 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998: ???refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.397→48.253 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.62
RfactorNum. reflection% reflection
Rfree0.2266 6493 5.51 %
Rwork0.1919 --
obs0.1938 117879 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137 Å2 / Biso mean: 50.5643 Å2 / Biso min: 16.83 Å2
Refinement stepCycle: final / Resolution: 2.397→48.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17076 0 215 570 17861
Biso mean--53.49 43.89 -
Num. residues----2187
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2634X-RAY DIFFRACTION6.469TORSIONAL
12D2634X-RAY DIFFRACTION6.469TORSIONAL
21A2490X-RAY DIFFRACTION6.469TORSIONAL
22C2490X-RAY DIFFRACTION6.469TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3967-2.42390.30431770.27193239341687
2.4239-2.45240.29221970.25163471366893
2.4524-2.48240.28572070.25143586379396
2.4824-2.51380.29332160.24853609382596
2.5138-2.54690.32241990.253559375895
2.5469-2.58170.28071880.23223596378495
2.5817-2.61860.26132020.228137173919100
2.6186-2.65770.27952170.23243733395099
2.6577-2.69920.31421930.24563739393299
2.6992-2.74350.32122000.241237703970100
2.7435-2.79080.30492260.2343711393799
2.7908-2.84150.29732290.225237443973100
2.8415-2.89620.25682350.21843715395099
2.8962-2.95530.26532350.21763705394099
2.9553-3.01950.26032350.210537553990100
3.0195-3.08980.26192290.210837533982100
3.0898-3.1670.24872080.2033658386697
3.167-3.25260.25772200.21937393959100
3.2526-3.34830.25952220.211837563978100
3.3483-3.45640.22752240.196937864010100
3.4564-3.57980.22092150.18433770398599
3.5798-3.72310.22642380.178937543992100
3.7231-3.89250.19482050.17137913996100
3.8925-4.09760.19311870.16193761394898
4.0976-4.35420.1832330.15693739397299
4.3542-4.69010.16572430.143638224065100
4.6901-5.16160.16872310.151338204051100
5.1616-5.90740.19322390.177738404079100
5.9074-7.43830.22442110.19043808401998
7.4383-48.26270.18962320.16873940417297
Refinement TLS params.Method: refined / Origin x: 17.0262 Å / Origin y: -44.6358 Å / Origin z: -26.577 Å
111213212223313233
T0.1188 Å2-0.0121 Å2-0.0172 Å2-0.2283 Å2-0.0166 Å2--0.2964 Å2
L0.1814 °20.068 °20.1785 °2-0.7621 °20.7329 °2--1.298 °2
S-0.0575 Å °-0.0202 Å °-0.0005 Å °-0.0283 Å °0.1031 Å °-0.0211 Å °-0.0387 Å °0.0899 Å °-0.0334 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 502
2X-RAY DIFFRACTION1allB2 - 502
3X-RAY DIFFRACTION1allC1 - 502
4X-RAY DIFFRACTION1allD1 - 431
5X-RAY DIFFRACTION1allE6 - 141
6X-RAY DIFFRACTION1allF1 - 384
7X-RAY DIFFRACTION1allM1 - 2
8X-RAY DIFFRACTION1allN1 - 2
9X-RAY DIFFRACTION1allH1
10X-RAY DIFFRACTION1allI1
11X-RAY DIFFRACTION1allS1 - 570
12X-RAY DIFFRACTION1allG1
13X-RAY DIFFRACTION1allJ1

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