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- PDB-4eb6: Tubulin-Vinblastine: Stathmin-like complex -

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Basic information

Entry
Database: PDB / ID: 4eb6
TitleTubulin-Vinblastine: Stathmin-like complex
Components
  • Stathmin-4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN/INHIBITOR / MICROTUBULES / TUBULIN / VINCA DOMAIN / VINBLASTINE / STATHMIN / STRUCTURAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / microtubule depolymerization / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / locomotory exploration behavior / startle response / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / microtubule-based process / response to mechanical stimulus / homeostasis of number of cells within a tissue / condensed chromosome / cellular response to calcium ion / tubulin binding / adult locomotory behavior / synapse organization / intracellular protein transport / neuron migration / neuromuscular junction / visual learning / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / cerebral cortex development / memory / recycling endosome / neuron projection development / gene expression / growth cone / neuron apoptotic process / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. ...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 / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-VLB / Tubulin beta chain / Tubulin alpha chain / Stathmin-4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsRanaivoson, F.M. / Gigant, B. / Knossow, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural plasticity of tubulin assembly probed by vinca-domain ligands.
Authors: Ranaivoson, F.M. / Gigant, B. / Berritt, S. / Joullie, M. / Knossow, M.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 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)220,48917
Polymers217,2175
Non-polymers3,27312
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20630 Å2
ΔGint-185 kcal/mol
Surface area68590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.690, 129.680, 252.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWZ0
#2: Protein Tubulin beta chain


Mass: 50043.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


Mass: 16719.938 Da / Num. of mol.: 1 / Fragment: unp residues 49-189 / Mutation: A58C, W64F
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 , 6 types, 43 molecules

#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: 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
#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
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN SEQUENCE WAS ...AUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT BECAUSE THE SEQUENCE OF OVINE BRAIN TUBULIN IS NOT AVAILABLE. FOR BETA-TUBULIN (CHAIN B AND CHAIN D), THERE ARE THREE MAJOR ISOTYPES EXPRESSED IN THE BRAIN. THEY MAINLY USED THE BETA 2B ISOTYPE SEQUENCE (NCBI NP_001003900.1), BUT INTRODUCED POINT MUTATIONS WHEN POSSIBLE TO TAKE INTO ACCOUNT THE ISOTYPE DIVERSITY. SPECIFICALLY, RESIDUE THR 33 IS FOUND IN 75% OF TUBULIN MOLECULES (25% IS SER). IT IS REFINED WITH THR BUT WITH AN 75% OCCUPANCY FOR THE CG2 ATOM. RESIDUE 172: MET (60%) OR VAL (40%), REFINED WITH MET, BUT WITH OCCUPANCY 0.6 FOR SDAND CE ATOMS. RESIDUE 220: A MIX OF THR (75%) AND ALA (25%), REFINED WITH THR, OCCUPANCY 0.75 FOR OG1 AND CG2 ATOMS. AT POSITION 277, A MIX OF SER (75%) AND ALA (25%), REFINED WITH SER BUT WITH OCCUPANCY O.75 FOR OG ATOM. RESIDUE 298: SAME AS ABOVE BUT WITH SER 60% AND ALA 40%, REFINED WITH SER BUT WITH OCCUPANCY O.60 FOR OG ATOM. POSITION 317: THR 25%, ALA 75%, REFINED WITH A THR BUT WITH AN 0.25 OCCUPANCY FOR THE OG1 AND CG2 ATOMS. RESIDUE 318: ILE (60%) OR VAL (40%), REFINED WITH ILE, WITH OCCUPANCY 0.6 FOR CD1 ATOM. RESIDUE 335: THE SAME AS ABOVE BUT WITH ILE 25% AND VAL 75%, REFINED WITH ILE, WITH OCCUPANCY 0.25 FOR CD1 ATOM. RESIDUE 375, A MIX OF ALA (0.75) AND SER (0.25) AT THIS POSITION, REFINED WITH SER, OCCUPANCY 0.25 FOR OG ATOM. THE STATHMIN-4 FRAGMENT (CHAIN E) USED IN THIS STUDY INCLUDES A N-TERMINAL ALA RESIDUE, HAS TWO POINT MUTATIONS (CYS14 TO ALA AND PHE20 TO TRP, STATHMIN NUMBERING).

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / pH: 6.8
Details: PEG, Li2SO4, PIPES, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.47→43.23 Å / Num. obs: 28253 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 89.57 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.2
Reflection shellResolution: 3.47→3.65 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.8 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.47→43.06 Å / Cor.coef. Fo:Fc: 0.9134 / Cor.coef. Fo:Fc free: 0.8939 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 1424 5.06 %RANDOM
Rwork0.2133 ---
obs0.2152 28150 --
Displacement parametersBiso mean: 174.25 Å2
Baniso -1Baniso -2Baniso -3
1--48.5159 Å20 Å20 Å2
2--30.3079 Å20 Å2
3---18.208 Å2
Refine analyzeLuzzati coordinate error obs: 1.211 Å
Refinement stepCycle: LAST / Resolution: 3.47→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14633 0 206 31 14870
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00815219HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.220673HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5295SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes426HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2193HARMONIC5
X-RAY DIFFRACTIONt_it15219HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion25.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1984SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18942SEMIHARMONIC4
LS refinement shellResolution: 3.47→3.6 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3096 157 5.32 %
Rwork0.2597 2795 -
all0.2622 2952 -
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)
12.4875-0.8928-0.20488.67093.27354.5383-0.27020.1529-0.35130.51020.8996-0.76920.58090.6758-0.62940.72280.1978-0.036-0.4481-0.3677-0.63849.387932.447274.366
21.1012-2.0541-0.33028.93953.12243.6493-0.1177-0.05970.30690.03670.7333-1.03920.34880.4808-0.61560.59130.1771-0.1213-0.3505-0.2952-0.50344.293872.115490.8848
32.4388-2.8744-0.3068.78533.62922.57540.2060.17350.2736-0.65430.2068-0.6078-0.01360.1781-0.41280.61470.1824-0.0937-0.4817-0.1678-0.5286-8.5972111.211105.15
43.3144-2.88660.13598.27651.24335.28210.49340.03550.7597-1.0773-0.4971-0.33890.04320.42690.0036-0.31740.00270.1755-0.4015-0.12860.0705-29.1799145.675117.467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|440 A|501 - A|502 E|4 - E|64 }
2X-RAY DIFFRACTION2{ B|1 - B|442 B|501 - B|501 E|65 - E|89 }
3X-RAY DIFFRACTION3{ C|1 - C|440 C|501 - C|502 E|90 - E|115 }
4X-RAY DIFFRACTION4{ D|1 - D|442 D|501 - D|501 E|116 - E|141 }

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