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- PDB-5fnv: a new complex structure of tubulin with an alpha-beta unsaturated... -

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Basic information

Entry
Database: PDB / ID: 5fnv
Titlea new complex structure of tubulin with an alpha-beta unsaturated lactone
Components
  • STATHMIN-4
  • TUBULIN ALPHA-1B CHAIN
  • TUBULIN BETA CHAIN
  • TUBULIN TYROSINE LIGASE
KeywordsSTRUCTURAL PROTEIN / TUBULIN COMPLEX ALPHA-BETA UNSATURATED LACTONE
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
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, 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 / 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 / PIRONETIN / Tubulin tyrosine ligase / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
RATTUS NORVEGICUS (Norway rat)
SUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsWang, Y. / Naismith, J. / Zhu, X.
CitationJournal: Nat.Commun. / Year: 2016
Title: Pironetin Reacts Covalently with Cysteine-316 of Alpha-Tubulin to Destabilize Microtubule.
Authors: Yang, J. / Wang, Y. / Wang, T. / Jiang, J. / Botting, C.H. / Liu, H. / Chen, Q. / Yang, J. / Naismith, J.H. / Zhu, X. / Chen, L.
History
DepositionNov 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Refinement description
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_label_seq_id / _struct_conn_type.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 CHAIN
C: TUBULIN ALPHA-1B CHAIN
D: TUBULIN BETA CHAIN
E: STATHMIN-4
F: TUBULIN TYROSINE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,89921
Polymers261,4476
Non-polymers3,45215
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.160, 157.200, 181.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALAA1 - 4371 - 437
21METMETVALVALCC1 - 4371 - 437
12ARGARGALAALABB2 - 4282 - 428
22ARGARGALAALADD2 - 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 / TUBULIN ALPHA SUBUNIT


Mass: 50204.445 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) / Strain (production host): BL21(DE3) / References: UniProt: Q2XVP4
#2: Protein TUBULIN BETA CHAIN / BETA-TUBULIN / TUBULIN BETA SUBUNIT


Mass: 49907.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02554
#3: Protein STATHMIN-4 / STATHMIN-LIKE PROTEIN B3 / RB3 / ISTATHMIN-4


Mass: 16844.162 Da / Num. of mol.: 1 / Fragment: STATHMIN-LIKE DOMAIN, RESIDUES 49-189 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / References: UniProt: P63043
#4: Protein TUBULIN TYROSINE LIGASE


Mass: 44378.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / References: UniProt: E1BQ43

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Non-polymers , 8 types, 83 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.: 3 / 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-X3H / PIRONETIN


Mass: 326.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H34O4
#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.: 68 / 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: 3.17 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 6.7
Details: 0.1M MES PH6.7;6% PEG4000 ;5% GLYCEROL;30MM CACL2;30MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853
DetectorType: DECTRIS 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: 2.61→45.49 Å / Num. obs: 88059 / % possible obs: 94.8 % / Observed criterion σ(I): 1.5 / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8
Reflection shellResolution: 2.61→2.68 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.6 / % possible all: 67.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I55

4i55


Resolution: 2.61→118.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 21.024 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.548 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22555 4397 5 %RANDOM
Rwork0.18575 ---
obs0.18773 83598 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.794 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.61→118.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16887 0 209 68 17164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01917617
X-RAY DIFFRACTIONr_bond_other_d0.0050.0216390
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.96323870
X-RAY DIFFRACTIONr_angle_other_deg1.249337747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50452145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66224.229849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.014152960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.18115109
X-RAY DIFFRACTIONr_chiral_restr0.0940.22600
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02119918
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024122
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0334.5668578
X-RAY DIFFRACTIONr_mcbond_other2.0294.5668577
X-RAY DIFFRACTIONr_mcangle_it3.1446.84410709
X-RAY DIFFRACTIONr_mcangle_other3.1456.84410710
X-RAY DIFFRACTIONr_scbond_it2.5364.859039
X-RAY DIFFRACTIONr_scbond_other2.4884.8459026
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7187.17213138
X-RAY DIFFRACTIONr_long_range_B_refined5.69336.18519082
X-RAY DIFFRACTIONr_long_range_B_other5.69536.18319081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A498000.11
12C498000.11
21B497080.09
22D497080.09
LS refinement shellResolution: 2.61→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 222 -
Rwork0.314 4323 -
obs--67.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.95910.1396-0.23183.26211.22142.55910.1267-0.06830.22190.16290.2787-0.1542-0.42320.3398-0.40540.15270.0040.08310.3424-0.16710.152325.48282.94461.422
21.4344-0.6416-0.52262.17311.812.9850.02920.10480.136-0.2195-0.14360.1208-0.3197-0.31050.11450.04650.0865-0.0390.3307-0.10930.070516.45157.47929.656
31.3487-0.16210.06661.85170.8471.6757-0.16180.06720.1242-0.14520.06420.0495-0.1609-0.0710.09760.0534-0.0585-0.0120.2604-0.04830.028313.1428.888-3.878
41.61230.0295-0.53381.60260.48622.1483-0.38180.6182-0.3265-0.55450.24-0.08780.3902-0.14990.14180.5055-0.27290.18820.5905-0.29580.16918.217-1.848-31.561
50.3991-0.5412-0.79453.81424.21415.2357-0.1282-0.03880.00640.39890.6047-0.55510.50260.7889-0.47650.12230.04020.05150.4791-0.20750.281539.94841.11620.24
61.78950.4764-1.81641.566-1.28224.2929-0.3111-0.2052-0.57840.28030.19650.02410.60830.13090.11460.52210.13920.13390.26860.07130.33062.88955.690.444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 437
2X-RAY DIFFRACTION2B2 - 428
3X-RAY DIFFRACTION3C1 - 439
4X-RAY DIFFRACTION4D2 - 430
5X-RAY DIFFRACTION5E6 - 140
6X-RAY DIFFRACTION6F1 - 384

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