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- PDB-1z2b: Tubulin-colchicine-vinblastine: stathmin-like domain complex -

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Basic information

Entry
Database: PDB / ID: 1z2b
TitleTubulin-colchicine-vinblastine: stathmin-like domain complex
Components
  • RB3 STATHMIN-LIKE DOMAIN 4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / COLCHICINE / GTPASE / MICROTUBULE / STATHMIN / TUBULIN / VINBLASTINE
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 / Chem-VLB / : / : / 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: 4.1 Å
AuthorsGigant, B. / Wang, C. / Ravelli, R.B.G. / Roussi, F. / Steinmetz, M.O. / Curmi, P.A. / Sobel, A. / Knossow, M.
CitationJournal: Nature / Year: 2005
Title: Structural basis for the regulation of tubulin by vinblastine.
Authors: Gigant, B. / Wang, C. / Ravelli, R.B. / Roussi, F. / Steinmetz, M.O. / Curmi, P.A. / Sobel, A. / Knossow, M.
History
DepositionMar 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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_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 / _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 (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. WE PRIMARY USED THE BOS TAURUS TUBULIN SEQUENCES (ALPHA: GB/59858433, BETA: GB50844501). BUT AS ONLY ONE ISOTYPE SEQUENCE IS REPORTED FOR BOVINE, THE FOLLOWING SUBSTITUTIONS HAVE BEEN INCORPORATED BASED ON THE KNOWN DIFFERENCES BETWEEN ISOTYPES IN OTHER SPECIES (E.G. IN MOUSE), ON THE RELATIVE EXPRESSION ON THESE ISOTYPES IN MAMMALIAN BRAIN (SEE BANERJEE ET AL. (1988) J BIOL CHEM, VOL 263, 3029-34, AND ALSO REDEKER ET AL. (1998) BIOCHEMISTRY, VOL 37, 14838-44), AND ON ELECTRON DENSITY: ON ALPHA CHAIN: V7I, M16I, T50N, C54S, I78V, N80T, P82T, P117L, S126A, S232G, A334T. ON BETA CHAIN: M172V, I318V.

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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: RB3 STATHMIN-LIKE DOMAIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,13814
Polymers216,4835
Non-polymers3,6559
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20060 Å2
ΔGint-116 kcal/mol
Surface area63740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)324.852, 324.852, 54.208
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
51A
61C
12B
22D
32B
42D
52B
62D

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
111ARGARGALAALAAA2 - 2402 - 240
211ARGARGALAALACC2 - 2402 - 240
321ILEILEARGARGAA265 - 320265 - 320
421ILEILEARGARGCC265 - 320265 - 320
531VALVALILEILEAA362 - 437362 - 437
631VALVALILEILECC362 - 437362 - 437
112ARGARGTHRTHRBB2 - 1682 - 166
212ARGARGTHRTHRDD2 - 1682 - 166
322THRTHRASNASNBB180 - 206178 - 204
422THRTHRASNASNDD180 - 206178 - 204
532ASNASNLEULEUBB228 - 428226 - 418
632ASNASNLEULEUDD228 - 428226 - 418

NCS ensembles :
ID
1
2
DetailsTHE ASYMETRIC UNIT CONTAINS ONE BIOGICAL ASSEMBLY WHICH CONSISTS IN TWO TUBULIN-HETERODIMERS AND ONE RB3-SLD

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha chain


Mass: 49947.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BRAIN / Source: (natural) Bos taurus (cattle) / Organ: BRAIN / References: GenBank: 59858433, UniProt: Q2HJ86*PLUS
#2: Protein Tubulin beta chain


Mass: 49937.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BRAIN / Source: (natural) Bos taurus (cattle) / Organ: BRAIN / References: GenBank: 50844501, UniProt: Q6B856*PLUS
#3: Protein RB3 STATHMIN-LIKE DOMAIN 4 / Stathmin-like protein B3 / RB3-SLD


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 , 5 types, 9 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-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
#8: Chemical ChemComp-VLB / (2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE / VINBLASTINE / Vinblastine


Mass: 810.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H58N4O9 / Comment: medication, chemotherapy*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: 3.81 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 291 K / pH: 7
Details: PEG, PIPES BUFFER, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K. THE CRYSTAL OF TUBULIN-COLCHICINE:RB3-SLD COMPLEX WAS SOAKED WITH A 2 MILLI-MOLAR VINBLASTINE SOLUTION FOR 24 HOURS., pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC / Detector: CCD / Date: Jun 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.1→40 Å / Num. obs: 25286 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.26 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25
Reflection shellResolution: 4.1→4.2 Å / Redundancy: 2.25 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.5 / % possible all: 76.6

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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: 4.1→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 57.032 / SU ML: 0.719 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.879 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL DUE TO THE LIMITED (4.1 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 (4.1 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 43 TO 46, 280 TO 284, 302 TO 306 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. FOR OTHER DETAILS SEE ALSO REMARK 999.
RfactorNum. reflection% reflectionSelection details
Rfree0.26886 1269 5.1 %RANDOM
Rwork0.20943 ---
obs0.21243 23765 95.39 %-
all-25034 --
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: 117.488 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.38 Å20 Å2
2---0.77 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 4.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13932 0 241 0 14173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02114453
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.9619678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.54151799
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_restr0.120.22171
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211111
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.30.27610
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2581
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2790.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.58999
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0214411
X-RAY DIFFRACTIONr_scbond_it035454
X-RAY DIFFRACTIONr_scangle_it04.55267
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
1A2666tight positional0.070.05
2B2992tight positional0.060.05
1A2666tight thermal00.5
2B2992tight thermal00.5
LS refinement shellResolution: 4.1→4.202 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.423 84
Rwork0.356 1375
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)
111.19011.81360.19753.6044-0.61993.31690.2498-0.77281.33360.1659-0.1824-0.2496-0.3343-0.0717-0.06740.9649-0.22260.13961.03860.09161.266133.944104.97917.482
212.35512.70471.55594.9315-0.18284.35650.28650.5952-0.4674-0.3713-0.2565-0.56110.27630.4472-0.02990.9958-0.19740.05491.48660.19460.6319100.78581.0624.634
313.49744.47860.60643.7089-0.54343.03070.29371.202-0.9505-0.56830.3418-0.5873-0.03730.6131-0.63551.2662-0.1555-0.56231.57390.14060.938362.8161.36-3.2
411.1852.033-0.24016.4438-0.36616.4136-0.18061.2250.2434-0.5857-0.31550.59040.0091-0.31130.49620.8784-0.0569-0.7271.51380.10990.831923.83648.062-6.257
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4372 - 437
2X-RAY DIFFRACTION1EE4 - 641 - 61
3X-RAY DIFFRACTION1AF5001
4X-RAY DIFFRACTION1AH6001
5X-RAY DIFFRACTION2BB2 - 4382 - 428
6X-RAY DIFFRACTION2EE65 - 8962 - 86
7X-RAY DIFFRACTION2BJ6021
8X-RAY DIFFRACTION2BL7001
9X-RAY DIFFRACTION2CN8001
10X-RAY DIFFRACTION3CC2 - 4372 - 437
11X-RAY DIFFRACTION3EE90 - 11587 - 112
12X-RAY DIFFRACTION3CG5011
13X-RAY DIFFRACTION3CI6011
14X-RAY DIFFRACTION4DD2 - 4382 - 428
15X-RAY DIFFRACTION4EE116 - 141113 - 138
16X-RAY DIFFRACTION4DK6031
17X-RAY DIFFRACTION4DM7011

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