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- PDB-1sa1: Tubulin-podophyllotoxin: stathmin-like domain complex -

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Basic information

Entry
Database: PDB / ID: 1sa1
TitleTubulin-podophyllotoxin: stathmin-like domain complex
Components
  • Stathmin 4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / COLCHICINE / GTPASE / MICROTUBULE PODOPHYLLOTOXIN / STATHMIN / TUBULIN
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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-POD / Tubulin alpha-1A chain / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1D chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsRavelli, R.B. / Gigant, B. / Curmi, P.A. / Jourdain, I. / Lachkar, S. / Sobel, A. / Knossow, M.
CitationJournal: Nature / Year: 2004
Title: Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain.
Authors: Ravelli, R.B. / Gigant, B. / Curmi, P.A. / Jourdain, I. / Lachkar, S. / Sobel, A. / Knossow, M.
History
DepositionFeb 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN ...SEQUENCE 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. AS THE SEQUENCE OF BOVINE BRAIN TUBULIN IS NOT AVAILABLE, THE PIG BRAIN TUBULIN SEQUENCE WAS USED AS A REFERENCE. ONE NOTICEABLE EXCEPTION IS RESIDUE ALPHA 265 WHICH IS COMMONLY ILE BUT ALA IN PIG ALPHA TUBULIN. ALPHA-TUBULIN AND BETA-TUBULIN HAVE BEEN ALIGNED AS IN NOGALES ET AL., NATURE VOL 391, PAGES 199-203. IN THIS ALIGNMENT, RESIDUES 45-46 AND 361-368 OF ALPHA-TUBULIN ARE MISSING IN BETA-TUBULIN. THE STATHMIN-LIKE DOMAIN OF RB3 (RB3-SLD) CORRESPONDS TO STAHMIN RESIDUES 5 TO 145 WITH THE ADDITION OF AN ALANINE AT THE N-TERMINUS, WHICH IS ACETYLATED. THE NUMBERING OF RB3-SLD IS ACCORDING TO THE STATHMIN SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha chain
B: Tubulin beta chain
C: Tubulin alpha chain
D: Tubulin beta chain
E: Stathmin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,66513
Polymers216,8555
Non-polymers2,8108
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18990 Å2
ΔGint-109.6 kcal/mol
Surface area68310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)328.061, 328.061, 54.301
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
112ARGARGTHRTHRBB2 - 2762 - 274
212ARGARGTHRTHRDD2 - 2762 - 274
322GLNGLNALAALABB282 - 438280 - 428
422GLNGLNASPASPDD282 - 437280 - 427

NCS ensembles :
ID
1
2
DetailsTHERE 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 (CHAIN E)

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha chain


Mass: 50163.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P02550, UniProt: Q2HJ86*PLUS
#2: Protein Tubulin beta chain


Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P02554, UniProt: Q6B856*PLUS
#3: Protein Stathmin 4 / / Stathmin-like protein B3 / RB3


Mass: 16712.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: STMN4 / Plasmid: pET-8c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02554, UniProt: P63043*PLUS

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Non-polymers , 4 types, 8 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: 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
#7: Chemical ChemComp-POD / 9-HYDROXY-5-(3,4,5-TRIMETHOXYPHENYL)-5,8,8A,9-TETRAHYDROFURO[3',4':6,7]NAPHTHO[2,3-D][1,3]DIOXOL-6(5AH)-ONE / PODOPHYLLOTOXIN / Podophyllotoxin


Mass: 414.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22O8 / Comment: toxin*YM

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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: 3.88 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, PIPES BUFFER, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Gigant, B., (2000) Cell, 102, 809.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
2PEG1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 / Wavelength: 0.933 Å
DetectorType: ADSC / Detector: CCD / Date: Jun 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 4.2→30 Å / Num. obs: 24624 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.26 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 4.2→4.3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2 / % possible all: 90.2
Reflection
*PLUS
Highest resolution: 4.2 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 4.2 Å / Lowest resolution: 4.3 Å / % possible obs: 90.2 %

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Processing

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

1sa0


Resolution: 4.2→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 56.857 / SU ML: 0.695 / Cross valid method: THROUGHOUT / ESU R Free: 0.873 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL DUE TO THE LIMITED (4.2 ANGSTROMS) RESOLUTION. IN ADDITION, THE FOLLOWING WEAKLY DEFINED RESIDUES ARE MISSING IN THIS ENTRY: ...Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL DUE TO THE LIMITED (4.2 ANGSTROMS) RESOLUTION. IN ADDITION, THE FOLLOWING WEAKLY DEFINED RESIDUES ARE MISSING IN THIS ENTRY: RESIDUES 40 TO 44 AND THE C-TERMINUS STARTING FROM RESIDUE 440 ON ALPHA TUBULIN CHAIN A, RESIDUES 277 TO 281 AND THE C-TERMINUS STARTING FROM RESIDUE 438 ON BETA TUBULIN CHAIN B, RESIDUES 39 TO 46 AND THE C-TERMINUS STARTING FROM RESIDUE 440 ON ALPHA TUBULIN CHAIN C, THE C-TERMINUS STARTING FROM RESIDUES 438 ON BETA TUBULIN CHAIN D, AND RESIDUES 4, 5, 43, 44 AND 142 TO 145 OF RB3-SLD. CA 5% OF THE SIDE CHAINS ARE POORLY DEFINED AND ARE CURRENTLY MODELLED AS ALANINES.
RfactorNum. reflection% reflectionSelection details
Rfree0.25935 1230 5 %RANDOM
Rwork0.20369 ---
all0.20643 ---
obs0.20643 23198 98.32 %-
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: 116.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-0.78 Å20 Å2
2---1.57 Å20 Å2
3---2.35 Å2
Refinement stepCycle: LAST / Resolution: 4.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13998 0 182 0 14180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02114508
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0911.9619763
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.52351832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1540.22192
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211197
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3230.27768
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.2646
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2190.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3480.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.0691.59172
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.12214642
X-RAY DIFFRACTIONr_scbond_it0.15635336
X-RAY DIFFRACTIONr_scangle_it0.2314.55121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3196tight positional0.070.05
2B3275tight positional0.060.05
1A3196tight thermal0.060.5
2B3275tight thermal0.050.5
LS refinement shellResolution: 4.204→4.308 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 83
Rwork0.344 1456
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)
19.33161.63560.24253.7485-0.25413.11470.1542-0.4161.01870.0043-0.0852-0.0062-0.31940.0416-0.06910.4572-0.13720.10420.446-0.03020.9461135.457104.91917.332
29.50891.99740.45854.6357-0.04084.11950.14490.0628-0.7354-0.3648-0.1127-0.2780.33910.1101-0.03220.4395-0.2072-0.05620.9010.17210.697102.43280.5775.063
39.68383.01590.11145.28670.34973.97190.22030.328-0.7728-0.39530.1387-0.57490.08570.4802-0.3590.6835-0.2534-0.39191.28370.26710.870563.96861.152-3.211
47.00471.4542-1.19015.8464-0.16237.15980.01250.5126-0.1779-0.2944-0.41490.77870.2675-0.18380.40240.4338-0.0195-0.65141.40030.07610.979624.847.615-6.138
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4392 - 439
2X-RAY DIFFRACTION1EE6 - 643 - 61
3X-RAY DIFFRACTION2BB2 - 4382 - 428
4X-RAY DIFFRACTION2EE65 - 8962 - 86
5X-RAY DIFFRACTION3CC2 - 4392 - 439
6X-RAY DIFFRACTION3EE90 - 11587 - 112
7X-RAY DIFFRACTION4DD2 - 4372 - 427
8X-RAY DIFFRACTION4EE116 - 141113 - 138

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