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- PDB-6o5n: Tubulin-RB3_SLD-TTL in complex with compound 10ab -

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Basic information

Entry
Database: PDB / ID: 6o5n
TitleTubulin-RB3_SLD-TTL in complex with compound 10ab
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 / 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 / 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 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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / 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 / 60s Ribosomal Protein L30; Chain: A; / 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 / 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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-QW9 / 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: 3.003 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: J.Med.Chem. / Year: 2019
Title: Structure-Guided Design, Synthesis, and Biological Evaluation of (2-(1H-Indol-3-yl)-1H-imidazol-4-yl)(3,4,5-trimethoxyphenyl) Methanone (ABI-231) Analogues Targeting the Colchicine Binding Site in Tubulin.
Authors: Wang, Q. / Arnst, K.E. / Wang, Y. / Kumar, G. / Ma, D. / White, S.W. / Miller, D.D. / Li, W. / Li, W.
History
DepositionMar 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)264,56419
Polymers261,3056
Non-polymers3,25913
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.301, 157.764, 182.084
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
11chain A
21(chain C and resid 1 through 437)
12(chain B and (resid 2 through 273 or resid 284 through 428))
22(chain D and resid 2 through 428)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETVALVALchain AAA1 - 4371 - 437
211METMETVALVAL(chain C and resid 1 through 437)CC1 - 4371 - 437
112ARGARGLEULEU(chain B and (resid 2 through 273 or resid 284 through 428))BB2 - 2732 - 273
122LEULEUALAALA(chain B and (resid 2 through 273 or resid 284 through 428))BB284 - 428284 - 428
212ARGARGALAALA(chain D and resid 2 through 428)DD2 - 4282 - 428

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 , 7 types, 54 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.: 3 / 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.: 2 / 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-QW9 / [2-(4-methyl-1H-indol-3-yl)-1H-imidazol-5-yl](3,4,5-trimethoxyphenyl)methanone


Mass: 391.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H21N3O4 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.89 Å3/Da / Density % sol: 57.5 %
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 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 61186 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 57.87 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.06 / Rrim(I) all: 0.15 / Χ2: 1 / Net I/σ(I): 3.7 / Num. measured all: 412131
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3-3.076.840030.5950.481.03100
3.07-3.156.640510.7150.3691.0371000.8820.958
3.15-3.236.140340.750.3141.06199.60.7220.789
3.23-3.336.540130.840.2451.04199.60.5850.635
3.33-3.437.240180.9070.191.05899.90.4720.509
3.43-3.567.240160.9380.1451.08999.90.3610.389
3.56-3.77.140530.9530.1161.0881000.2880.311
3.7-3.87740740.9710.0911.0941000.2220.24
3.87-4.076.940470.9810.0731.0881000.1780.193
4.07-4.336.840740.9840.061.0611000.1450.157
4.33-4.666.440760.9850.0511.06299.90.1190.13
4.66-5.136.441050.9870.0460.96999.80.1070.117
5.13-5.877.141290.9870.0440.8911000.1080.117
5.87-7.396.841310.9910.0380.78499.80.0910.099
7.39-506.343620.9960.0260.64499.70.060.066

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.003→41.784 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.73
RfactorNum. reflection% reflection
Rfree0.2452 2940 4.99 %
Rwork0.2024 --
obs0.2046 58896 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.47 Å2 / Biso mean: 65.0109 Å2 / Biso min: 19.61 Å2
Refinement stepCycle: final / Resolution: 3.003→41.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17228 0 207 41 17476
Biso mean--48.52 47.3 -
Num. residues----2178
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2616X-RAY DIFFRACTION6.831TORSIONAL
12C2616X-RAY DIFFRACTION6.831TORSIONAL
21B2490X-RAY DIFFRACTION6.831TORSIONAL
22D2490X-RAY DIFFRACTION6.831TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0031-3.05230.3609970.31061850194767
3.0523-3.10490.35661110.29682192230380
3.1049-3.16130.32451340.28132419255389
3.1613-3.22210.34061460.27642499264593
3.2221-3.28790.30531430.26842634277795
3.2879-3.35930.33281210.25052710283199
3.3593-3.43740.25551250.241227482873100
3.4374-3.52340.29681510.232427272878100
3.5234-3.61860.29681360.220727402876100
3.6186-3.7250.24761550.211527322887100
3.725-3.84510.25491410.198127502891100
3.8451-3.98250.23331290.188227822911100
3.9825-4.14180.22361500.181427572907100
4.1418-4.33010.21881360.174127632899100
4.3301-4.55810.17221400.164227842924100
4.5581-4.84330.20461480.1627492897100
4.8433-5.21660.20121450.17327782923100
5.2166-5.74040.25021570.192928092966100
5.7404-6.56830.251640.206527902954100
6.5683-8.26480.23811540.18822816297099
8.2648-41.78790.2161570.18882927308498
Refinement TLS params.Method: refined / Origin x: 17.1936 Å / Origin y: -44.1111 Å / Origin z: -26.5499 Å
111213212223313233
T0.1256 Å2-0.0354 Å2-0.011 Å2-0.2917 Å2-0.0367 Å2--0.3219 Å2
L0.2644 °20.0561 °20.2043 °2-0.8134 °20.7176 °2--1.306 °2
S-0.0524 Å °0.0104 Å °-0.031 Å °-0.0891 Å °0.1276 Å °-0.0152 Å °-0.0831 Å °0.086 Å °-0.0543 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 437
2X-RAY DIFFRACTION1allA501 - 502
3X-RAY DIFFRACTION1allB2 - 428
4X-RAY DIFFRACTION1allB501 - 502
5X-RAY DIFFRACTION1allC1 - 440
6X-RAY DIFFRACTION1allC501 - 502
7X-RAY DIFFRACTION1allD1 - 431
8X-RAY DIFFRACTION1allE6 - 141
9X-RAY DIFFRACTION1allF1 - 380
10X-RAY DIFFRACTION1allL1
11X-RAY DIFFRACTION1allM1 - 2
12X-RAY DIFFRACTION1allN1 - 2
13X-RAY DIFFRACTION1allG1 - 2
14X-RAY DIFFRACTION1allH1 - 43

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