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- PDB-3du7: Tubulin-colchicine-phomopsin A: Stathmin-like domain complex -

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Basic information

Entry
Database: PDB / ID: 3du7
TitleTubulin-colchicine-phomopsin A: Stathmin-like domain complex
Components
  • Stathmin-4
  • Tubulin alpha-1C chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / alpha-tubulin / beta-tubulin / colchicine / gtpase / microtubule / phomopsin A / stathmin / tubulin / GTP-binding / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton ...positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / nervous system development / growth cone / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site ...Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 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
Similarity search - Domain/homology
Chem-CN2 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Phomopsin A / Stathmin-4 / Tubulin alpha-1C chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsCormier, A. / Marchand, M. / Ravelli, R.B. / Knossow, M. / Gigant, B.
CitationJournal: Embo Rep. / Year: 2008
Title: Structural insight into the inhibition of tubulin by vinca domain peptide ligands
Authors: Cormier, A. / Marchand, M. / Ravelli, R.B. / Knossow, M. / Gigant, B.
History
DepositionJul 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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-1C chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1C chain
D: Tubulin beta-2B chain
E: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,25215
Polymers216,8295
Non-polymers4,42310
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19020 Å2
ΔGint-109 kcal/mol
Surface area65900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)327.126, 327.126, 53.672
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31A
41C
12B
22D
32B
42D

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGARGARGAA2 - 2432 - 243
211ARGARGARGARGCC2 - 2432 - 243
321THRTHRSERSERAA257 - 439257 - 439
421THRTHRSERSERCC257 - 439257 - 439
112ARGARGLEULEUBB2 - 2752 - 273
212ARGARGLEULEUDD2 - 2752 - 273
322ARGARGASPASPBB284 - 437282 - 427
422ARGARGASPASPDD284 - 437282 - 427

NCS ensembles :
ID
1
2

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha-1C chain / tubulin alpha chain


Mass: 50088.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: brain / References: UniProt: Q3ZCJ7
#2: Protein Tubulin beta-2B chain / tubulin beta chain


Mass: 49969.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: brain / References: UniProt: Q6B856
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


Mass: 16712.967 Da / Num. of mol.: 1 / Fragment: RB3 stathmin-like domain 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Plasmid: PET-8C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63043

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Non-polymers , 5 types, 10 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CN2 / 2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE


Mass: 431.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25NO6S
#6: Chemical ChemComp-HOS / Phomopsin A


Mass: 789.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H45ClN6O12
#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Details

Sequence detailsTHERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN HETERODIMERS ...THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN HETERODIMERS (CHAINS A-B AND C-D), AND ONE STATHMIN-LIKE DOMAIN OF RB3 (RB3-SLD) WHICH CORRESPONDS TO STAHMIN RESIDUES 5 TO 145 WITH THE ADDITION OF ONE ACETYLATED ALANINE AT THE N-TERMINUS. THE NUMBERING OF RB3-SLD IS ACCORDING TO THE STATHMIN SEQUENCE. ALPHA- TUBULIN AND BETA-TUBULIN HAVE BEEN ALIGNED AS IN NOGALES ET AL., NATURE VOL 391,199-203. IN THIS ALIGNMENT, RESIDUES 45-46 AND 361-368 OF ALPHA-TUBULIN ARE MISSING IN BETA- TUBULIN. THERE ARE SEVERAL EXPRESSED TUBULIN ISOTYPES IN MAMMALIAN BRAIN. WE USED THE BOS TAURUS TUBULIN SEQUENCE OF THE MOST ABUNDANT ISOTYPES (ALPHA: ISOTYPE 1, GI:73586894, BETA: ISOTYPE 2, GI:51491829) BUT WITH THE ILE TO VAL SUBSTITUTION AT POSITION 318 ON BETA TUBULIN.

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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: 3.82 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, PIPES BUFFER. The crystal of tubulin-colchicine:RB3-SLD complex was soaked with a 0.7mM Phomopsin A solution for 24 hours., pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976 / Wavelength: 0.976 Å
DetectorType: ADSC / Detector: CCD / Date: Jul 3, 2003
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 4.1→40 Å / Num. all: 26640 / Num. obs: 25575 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.078 / Net I/σ(I): 12.2
Reflection shellResolution: 4.1→4.2 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.428 / % possible all: 90.8

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SA0

1sa0


Resolution: 4.1→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 65.918 / SU ML: 0.784 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.86 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Care should be exercised in interpreting the current model due to the limited (4.1 angstroms) resolution.
RfactorNum. reflection% reflectionSelection details
Rfree0.26471 1277 5 %RANDOM
Rwork0.21521 ---
all0.21781 26330 --
obs0.21781 25389 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 95.778 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å21.77 Å20 Å2
2--3.55 Å20 Å2
3----5.32 Å2
Refinement stepCycle: LAST / Resolution: 4.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13966 0 292 0 14258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02114583
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.9619873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.77451833
X-RAY DIFFRACTIONr_chiral_restr0.1310.22185
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211309
X-RAY DIFFRACTIONr_nbd_refined0.3050.28101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2648
X-RAY DIFFRACTIONr_metal_ion_refined0.5740.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3850.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4490.22
X-RAY DIFFRACTIONr_mcbond_it01.59145
X-RAY DIFFRACTIONr_mcangle_it0214597
X-RAY DIFFRACTIONr_scbond_it035438
X-RAY DIFFRACTIONr_scangle_it04.55275
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3114tight positional0.070.05
2B3170tight positional0.060.05
1A3114tight thermal00.5
2B3170tight thermal00.5
LS refinement shellResolution: 4.1→4.202 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.457 85
Rwork0.415 1579
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)
19.310.74140.40893.7397-0.23982.73070.3313-0.39050.87920.1902-0.18850.0397-0.43710.0717-0.14280.7402-0.23750.15020.87990.12931.3701134.965105.03816.588
28.11761.80130.37554.9741-0.26614.60140.3047-0.1748-0.518-0.1036-0.2085-0.22750.25060.3135-0.09630.6614-0.25810.00791.21360.22591.0843102.1680.9324.468
310.56552.9539-1.0444.29990.25763.45980.22060.256-0.6378-0.33170.1518-0.1370.03070.2211-0.37240.8047-0.2032-0.41891.41820.4161.565563.85960.791-2.668
48.7922.9771-0.09225.51530.68118.60080.3170.51660.2590.398-0.87140.76030.575-0.69930.55440.3653-0.0833-0.68261.85220.15431.275724.48548.231-5.809
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4392 - 439
2X-RAY DIFFRACTION1EE4 - 641 - 61
3X-RAY DIFFRACTION1AF5001
4X-RAY DIFFRACTION1DH6001
5X-RAY DIFFRACTION2BB2 - 4372 - 427
6X-RAY DIFFRACTION2EE65 - 8962 - 86
7X-RAY DIFFRACTION2DH6023
8X-RAY DIFFRACTION2BI7001
9X-RAY DIFFRACTION2BK8001
10X-RAY DIFFRACTION3CC2 - 4392 - 439
11X-RAY DIFFRACTION3EE90 - 11587 - 112
12X-RAY DIFFRACTION3CG5011
13X-RAY DIFFRACTION3DH6012
14X-RAY DIFFRACTION4DD2 - 4372 - 427
15X-RAY DIFFRACTION4EE116 - 141113 - 138
16X-RAY DIFFRACTION4DH6034
17X-RAY DIFFRACTION4DJ7011
18X-RAY DIFFRACTION4DL8011

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