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- PDB-1sa0: TUBULIN-COLCHICINE: STATHMIN-LIKE DOMAIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1sa0
TitleTUBULIN-COLCHICINE: 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 / motile cilium / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development ...positive regulation of axon guidance / microtubule depolymerization / motile cilium / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / 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 / 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. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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. / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 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 / 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
Chem-CN2 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.58 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 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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_struct_conn_angle / struct_conn / 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_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.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 / _struct_conn.pdbx_dist_value / _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_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_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 ONE 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)219,72414
Polymers216,8555
Non-polymers2,8699
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19070 Å2
ΔGint-114 kcal/mol
Surface area64930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)328.690, 328.691, 54.679
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
321THRTHRVALVALAA257 - 437257 - 437
421THRTHRVALVALCC257 - 437257 - 437
112ARGARGPROPROBB2 - 2742 - 272
212ARGARGPROPRODD2 - 2742 - 272
322LEULEULEULEUBB286 - 428284 - 418
422LEULEULEULEUDD286 - 428284 - 418

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

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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 (domestic 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 (domestic 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: P63043

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Non-polymers , 4 types, 9 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#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-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
#7: 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

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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: 3.93 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: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC / Detector: CCD / Date: Nov 3, 2001
RadiationProtocol: MIRAS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 41752 / % possible obs: 0.966 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062
Reflection shellResolution: 3.5→3.58 Å / Rmerge(I) obs: 0.639 / % possible all: 0.9
Reflection
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 40 Å / Num. obs: 41617 / % possible obs: 96.4 %
Reflection shell
*PLUS
% possible obs: 82.4 % / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
DMmodel building
REFMAC5.1.24refinement
DMphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.58→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.931 / SU B: 33.422 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.553
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL DUE TO THE LIMITED (3.58 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 (3.58 ANGSTROMS) RESOLUTION. IN ADDITION, THE FOLLOWING WEAKLY DEFINED RESIDUES ARE MISSING IN THIS ENTRY: RESIDUES 38 TO 46 AND THE C-TERMINUS STARTING FROM RESIDUE 438 ON ALPHA TUBULIN CHAIN A, RESIDUES 278 TO 285 AND THE C-TERMINUS STARTING FROM RESIDUE 439 ON BETA TUBULIN CHAIN B, RESIDUES 37 TO 46, 280 TO 284, AND THE THE C-TERMINUS STARTING FROM RESIDUE 438 ON ALPHA TUBULIN CHAIN C, RESIDUES 278 TO 285 AND THE C-TERMINUS STARTING FROM RESIDUES 439 ON BETA TUBULIN CHAIN D, AND RESIDUES 31 TO 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
Rfree0.24852 2042 5.1 %RANDOM
Rwork0.23166 ---
all0.23252 ---
obs0.23252 38029 98.79 %-
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: 83.054 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.44 Å20 Å2
2--0.89 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 3.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13891 0 183 0 14074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02114384
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.95419570
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.14851798
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_restr0.1380.22161
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211067
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2860.26934
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2466
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1730.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3370.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it01.58994
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0214414
X-RAY DIFFRACTIONr_scbond_it035390
X-RAY DIFFRACTIONr_scangle_it04.55156
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
1A3060tight positional0.050.05
2B3216tight positional0.040.05
1A3060tight thermal00.5
2B3216tight thermal00.5
LS refinement shellResolution: 3.58→3.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 135
Rwork0.365 2530
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)
17.4640.7230.28383.1906-0.1062.82070.0868-0.33240.76080.025-0.1473-0.2677-0.22910.07610.06050.3413-0.13970.06210.51760.01150.6192136.126104.79616.916
28.1971.9446-0.45823.9983-0.47613.872-0.09260.1171-0.6302-0.3351-0.07-0.37490.54170.04280.16260.4252-0.1643-0.02071.01910.07940.3807103.42380.0744.65
38.3581.8735-0.43624.0163-0.39013.4950.0240.415-0.4951-0.33840.1323-0.66990.11520.6136-0.15630.4361-0.1656-0.20061.1560.1390.612964.87260.262-2.935
47.86451.1417-0.54084.5023-0.46845.40190.01830.4949-0.1528-0.2767-0.21680.28360.4711-0.03440.19850.343-0.0365-0.39531.09150.09090.563225.49546.997-5.531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4372 - 437
2X-RAY DIFFRACTION1EE4 - 301 - 27
3X-RAY DIFFRACTION2BB2 - 4382 - 428
4X-RAY DIFFRACTION2EE65 - 8962 - 86
5X-RAY DIFFRACTION3CC2 - 4372 - 437
6X-RAY DIFFRACTION3EE90 - 11587 - 112
7X-RAY DIFFRACTION4DD2 - 4382 - 428
8X-RAY DIFFRACTION4EE116 - 141113 - 138
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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