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- PDB-5jcb: Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1 -

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Basic information

Entry
Database: PDB / ID: 5jcb
TitleMicrotubule depolymerizing agent podophyllotoxin derivative YJTSF1
Components
  • Stathmin
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin-Tyrosine Ligase
KeywordsSTRUCTURAL PROTEIN / microtubule destabilization / podophyllum
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 / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #11480 / 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 ...Rossmann fold - #11480 / 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. / ATP-grasp fold, A 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. / 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 / Dna Ligase; domain 1 / 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 / IMIDAZOLE / Chem-NV4 / DI(HYDROXYETHYL)ETHER / Tubulin tyrosine ligase / Stathmin-4 / Tubulin beta chain / Tubulin beta chain / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuan, Z. / Zhao, W. / Yin, P.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structural Insights into the Inhibition of Tubulin by the Antitumor Agent 4 beta-(1,2,4-triazol-3-ylthio)-4-deoxypodophyllotoxin.
Authors: Zhao, W. / Zhou, C. / Guan, Z.Y. / Yin, P. / Chen, F. / Tang, Y.J.
History
DepositionApr 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
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 / 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_label_seq_id / _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.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 chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin
F: Tubulin-Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,27236
Polymers263,3666
Non-polymers4,90630
Water10,034557
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24870 Å2
ΔGint-161 kcal/mol
Surface area78890 Å2
Unit cell
Length a, b, c (Å)104.357, 157.252, 179.631
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 natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5B2, UniProt: P02554*PLUS
#3: Protein Stathmin


Mass: 18060.414 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 49-189 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z508
#4: Protein Tubulin-Tyrosine Ligase


Mass: 44897.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E1BQ43*PLUS

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Non-polymers , 12 types, 587 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.: 7 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#12: 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
#13: Chemical ChemComp-NV4 / (5R,5aR,8aS,9R)-9-[(4H-1,2,4-triazol-3-yl)sulfanyl]-5-(3,4,5-trimethoxyphenyl)-5,8,8a,9-tetrahydro-2H-furo[3',4':6,7]naphtho[2,3-d][1,3]dioxol-6(5aH)-one


Mass: 497.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N3O7S
#14: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#15: 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
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsIn chains B/D, residue numbers 43, 44, 361-368 are simply skipped.

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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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, Glycerol, Magnesium chloride, Calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 131984 / % possible obs: 99.9 % / Redundancy: 7.4 % / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4T

4i4t


Resolution: 2.3→47.636 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 6500 4.95 %
Rwork0.1813 --
obs0.1822 131273 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17043 0 309 557 17909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817964
X-RAY DIFFRACTIONf_angle_d1.03524402
X-RAY DIFFRACTIONf_dihedral_angle_d21.4566709
X-RAY DIFFRACTIONf_chiral_restr0.0632670
X-RAY DIFFRACTIONf_plane_restr0.0053146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.29962030.2734122X-RAY DIFFRACTION99
2.3261-2.35350.28962070.26344106X-RAY DIFFRACTION100
2.3535-2.38220.28562230.25364117X-RAY DIFFRACTION99
2.3822-2.41240.29822210.24654092X-RAY DIFFRACTION100
2.4124-2.44410.26812270.24194110X-RAY DIFFRACTION99
2.4441-2.47760.26771760.22754155X-RAY DIFFRACTION100
2.4776-2.5130.27072100.23534103X-RAY DIFFRACTION100
2.513-2.55050.26072300.23544127X-RAY DIFFRACTION100
2.5505-2.59030.29932130.22714103X-RAY DIFFRACTION100
2.5903-2.63280.23082190.2284118X-RAY DIFFRACTION100
2.6328-2.67820.25372180.21274127X-RAY DIFFRACTION100
2.6782-2.72690.25632050.2144142X-RAY DIFFRACTION100
2.7269-2.77930.2462170.20434127X-RAY DIFFRACTION100
2.7793-2.83610.22992160.20614143X-RAY DIFFRACTION100
2.8361-2.89770.22522340.19884154X-RAY DIFFRACTION100
2.8977-2.96510.22662190.2024123X-RAY DIFFRACTION100
2.9651-3.03920.22112100.19894141X-RAY DIFFRACTION100
3.0392-3.12140.21652070.19434131X-RAY DIFFRACTION100
3.1214-3.21320.20372190.19314176X-RAY DIFFRACTION100
3.2132-3.31690.19712110.18254160X-RAY DIFFRACTION100
3.3169-3.43540.20452480.17814138X-RAY DIFFRACTION100
3.4354-3.5730.18992300.16684165X-RAY DIFFRACTION100
3.573-3.73550.19972220.16254181X-RAY DIFFRACTION100
3.7355-3.93240.16692080.1534179X-RAY DIFFRACTION100
3.9324-4.17860.16472240.14584185X-RAY DIFFRACTION100
4.1786-4.5010.14012260.13594181X-RAY DIFFRACTION100
4.501-4.95350.14142120.13114218X-RAY DIFFRACTION100
4.9535-5.66930.15952320.16074223X-RAY DIFFRACTION100
5.6693-7.13890.20361960.18114310X-RAY DIFFRACTION100
7.1389-47.64660.16482170.17334416X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -17.6346 Å / Origin y: 43.751 Å / Origin z: -25.9191 Å
111213212223313233
T0.143 Å2-0.0136 Å20.0118 Å2-0.2059 Å20.0257 Å2--0.2788 Å2
L0.1363 °20.0105 °2-0.0742 °2-0.5254 °2-0.554 °2--0.9659 °2
S-0.027 Å °-0.0088 Å °0.0101 Å °-0.0318 Å °0.0837 Å °0.0119 Å °0.0214 Å °-0.0775 Å °-0.0511 Å °
Refinement TLS groupSelection details: all

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