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- PDB-5ca1: Crystal structure of T2R-TTL-Nocodazole complex -

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Basic information

Entry
Database: PDB / ID: 5ca1
TitleCrystal structure of T2R-TTL-Nocodazole complex
Components
  • Stathmin-4
  • Tubulin alpha
  • Tubulin beta-2 chain
  • Uncharacterized protein
KeywordsSTRUCTURAL PROTEIN / Inhibitor / Complex / Tubulin
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / microtubule depolymerization / negative regulation of microtubule polymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase activity / microtubule depolymerization / negative regulation of microtubule polymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle / growth cone / microtubule / hydrolase activity / neuron projection / nucleotide binding / GTPase activity / calcium ion binding / 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. / 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; / 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 / Dna Ligase; domain 1 / 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 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / nocodazole / Tubulin alpha chain / Tubulin tyrosine ligase / Tubulin beta-2 chain / Stathmin-4
Similarity search - Component
Biological speciesGallus gallus (chicken)
Rattus norvegicus (Norway rat)
Sus barbatus (bearded pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsWang, Y. / Yu, Y. / Chen, Q. / Yang, J.
CitationJournal: Febs J. / Year: 2016
Title: Structures of a diverse set of colchicine binding site inhibitors in complex with tubulin provide a rationale for drug discovery.
Authors: Wang, Y. / Zhang, H. / Gigant, B. / Yu, Y. / Wu, Y. / Chen, X. / Lai, Q. / Yang, Z. / Chen, Q. / Yang, J.
History
DepositionJun 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_oper_list / struct_conn
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.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_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha
B: Tubulin beta-2 chain
C: Tubulin alpha
D: Tubulin beta-2 chain
E: Stathmin-4
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,98121
Polymers261,3056
Non-polymers3,67615
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23100 Å2
ΔGint-110 kcal/mol
Surface area79920 Å2
Unit cell
Length a, b, c (Å)105.440, 158.362, 180.692
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


Mass: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus barbatus (bearded pig) / References: UniProt: A0A0R4I993*PLUS
#2: Protein Tubulin beta-2 chain / Beta-tubulin class-II


Mass: 49999.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P32882
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 49-189
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 Uncharacterized protein / TUBULIN TYROSINE LIGASE / TTL


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 , 9 types, 392 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-NZO / nocodazole / methyl [6-(thiophen-2-ylcarbonyl)-1H-benzimidazol-2-yl]carbamate


Mass: 301.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11N3O3S / Comment: antineoplastic*YM
#12: 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
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% polyethylene glycol 4000, 8% glycerol, 0.1M 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: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 118147 / % possible obs: 100 % / Redundancy: 6.8 % / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I55

4i55


Resolution: 2.401→41.523 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2249 5838 4.94 %
Rwork0.1915 --
obs0.1932 118139 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→41.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17267 0 228 377 17872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417877
X-RAY DIFFRACTIONf_angle_d0.86624233
X-RAY DIFFRACTIONf_dihedral_angle_d15.5566610
X-RAY DIFFRACTIONf_chiral_restr0.0372630
X-RAY DIFFRACTIONf_plane_restr0.0043137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.401-2.42830.33122000.25523579X-RAY DIFFRACTION98
2.4283-2.45680.29292050.24373712X-RAY DIFFRACTION100
2.4568-2.48680.29761800.23893688X-RAY DIFFRACTION100
2.4868-2.51820.29561970.23973744X-RAY DIFFRACTION100
2.5182-2.55140.27311940.23253718X-RAY DIFFRACTION100
2.5514-2.58630.29652040.22663682X-RAY DIFFRACTION100
2.5863-2.62330.27551860.22513721X-RAY DIFFRACTION100
2.6233-2.66240.282100.23073695X-RAY DIFFRACTION100
2.6624-2.7040.27971970.22973731X-RAY DIFFRACTION100
2.704-2.74830.27162030.22613683X-RAY DIFFRACTION100
2.7483-2.79570.25131580.22833762X-RAY DIFFRACTION100
2.7957-2.84650.28252140.22033690X-RAY DIFFRACTION100
2.8465-2.90130.27671770.23093742X-RAY DIFFRACTION100
2.9013-2.96050.30051980.22993739X-RAY DIFFRACTION100
2.9605-3.02480.28471800.22613733X-RAY DIFFRACTION100
3.0248-3.09520.26552090.2193705X-RAY DIFFRACTION100
3.0952-3.17260.24641950.22143760X-RAY DIFFRACTION100
3.1726-3.25830.25091730.22983727X-RAY DIFFRACTION100
3.2583-3.35410.26761950.21943731X-RAY DIFFRACTION100
3.3541-3.46240.23551990.21033751X-RAY DIFFRACTION100
3.4624-3.5860.21681750.19983762X-RAY DIFFRACTION100
3.586-3.72950.20721700.18823765X-RAY DIFFRACTION100
3.7295-3.89910.19612030.17453754X-RAY DIFFRACTION100
3.8991-4.10450.20331840.16733773X-RAY DIFFRACTION100
4.1045-4.36140.17392130.1583755X-RAY DIFFRACTION100
4.3614-4.69780.17482120.14163756X-RAY DIFFRACTION100
4.6978-5.16970.17692100.15143778X-RAY DIFFRACTION100
5.1697-5.9160.19022000.16993815X-RAY DIFFRACTION100
5.916-7.44650.21181780.18493886X-RAY DIFFRACTION100
7.4465-41.52890.19522190.15713964X-RAY DIFFRACTION99

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