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- PDB-5xaf: Crystal structure of tubulin-stathmin-TTL-Compound Z1 complex -

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Basic information

Entry
Database: PDB / ID: 5xaf
TitleCrystal structure of tubulin-stathmin-TTL-Compound Z1 complex
Components
  • Stathmin-4
  • TTL Protein
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsSTRUCTURAL PROTEIN / Tubulin
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / tubulin binding / spindle microtubule / protein modification process ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / cilium / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Helix hairpin bin / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / 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 / Helix hairpin bin / 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. / ATP-grasp fold, A domain / 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. / Dna Ligase; domain 1 / 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
Chem-84F / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / IMIDAZOLE / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Rattus norvegicus (Norway rat)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.551 Å
AuthorsZhang, H. / Luo, C. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Eur J Med Chem / Year: 2017
Title: Design, synthesis, biological evaluation and cocrystal structures with tubulin of chiral beta-lactam bridged combretastatin A-4 analogues as potent antitumor agents
Authors: Zhou, P. / Liang, Y. / Zhang, H. / Jiang, H. / Feng, K. / Xu, P. / Wang, J. / Wang, X. / Ding, K. / Luo, C. / Liu, M. / Wang, Y.
History
DepositionMar 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.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: TTL Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,01837
Polymers266,0846
Non-polymers4,93431
Water13,277737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26210 Å2
ΔGint-147 kcal/mol
Surface area78820 Å2
Unit cell
Length a, b, c (Å)104.568, 156.509, 182.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.) Bos taurus (domestic cattle) / Production host: Bos taurus (domestic cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: TUBB2B / Production host: Bos taurus (domestic cattle) / References: UniProt: Q6B856
#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 TTL Protein


Mass: 43549.625 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 , 10 types, 768 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#9: 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
#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-84F / (3S,4R)-4-(3-hydroxy-4-methoxyphenyl)-3-methyl-1-(3,4,5-trimethoxyphenyl)azetidin-2-one


Mass: 373.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23NO6
#12: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#13: 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
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 6% PEG 4000, 8% glycerol, 100mM MES, 30mM CaCl2, 30mM MgCl2, pH 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.551→49.767 Å / Num. obs: 97756 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 18.72

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4o2b

4o2b


Resolution: 2.551→49.767 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 1999 2.05 %
Rwork0.2065 --
obs0.2075 97742 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.551→49.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17086 0 312 737 18135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817964
X-RAY DIFFRACTIONf_angle_d1.02524389
X-RAY DIFFRACTIONf_dihedral_angle_d16.80910776
X-RAY DIFFRACTIONf_chiral_restr0.0552660
X-RAY DIFFRACTIONf_plane_restr0.0063150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5508-2.61460.41211400.36286759X-RAY DIFFRACTION100
2.6146-2.68530.37871420.35786740X-RAY DIFFRACTION100
2.6853-2.76430.39811410.33746764X-RAY DIFFRACTION100
2.7643-2.85350.33751410.31896768X-RAY DIFFRACTION100
2.8535-2.95550.32771410.30696758X-RAY DIFFRACTION100
2.9555-3.07380.3671430.29746818X-RAY DIFFRACTION100
3.0738-3.21370.31821410.27696760X-RAY DIFFRACTION100
3.2137-3.38310.34421420.26076832X-RAY DIFFRACTION100
3.3831-3.5950.28181420.23026801X-RAY DIFFRACTION100
3.595-3.87240.2231430.20096847X-RAY DIFFRACTION100
3.8724-4.2620.25271430.17096840X-RAY DIFFRACTION100
4.262-4.87820.20691450.14376900X-RAY DIFFRACTION100
4.8782-6.14420.20881450.17236967X-RAY DIFFRACTION100
6.1442-49.77660.20271500.16077189X-RAY DIFFRACTION100

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