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- PDB-4f6r: Tubulin:Stathmin-like domain complex -

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Basic information

Entry
Database: PDB / ID: 4f6r
TitleTubulin:Stathmin-like domain complex
Components
  • Designed ankyrin repeat protein (DARPIN) D2
  • Stathmin-like domain R1
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / GTPASE / MICROTUBULE / RB3 / STATHMIN S-TUBULIN / SUBTILISIN / TUBULIN
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 / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / startle response / microtubule polymerization / locomotory exploration behavior / 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 / adult locomotory behavior / synapse organization / intracellular protein transport / neuron migration / visual learning / neuromuscular junction / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / memory / recycling endosome / cerebral cortex development / gene expression / neuron apoptotic process / microtubule / hydrolase activity / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin ...Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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 / Tubulin beta chain / Tubulin alpha chain
Similarity search - Component
Biological speciesArtificial gene (others)
OVIS ARIES (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsGigant, B. / Mignot, I. / Knossow, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Design and characterization of modular scaffolds for tubulin assembly.
Authors: Mignot, I. / Pecqueur, L. / Dorleans, A. / Karuppasamy, M. / Ravelli, R.B. / Dreier, B. / Pluckthun, A. / Knossow, M. / Gigant, B.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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_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.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_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: Stathmin-like domain R1
D: Designed ankyrin repeat protein (DARPIN) D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,7889
Polymers128,5064
Non-polymers1,2825
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.060, 75.570, 155.680
Angle α, β, γ (deg.)90.00, 96.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) OVIS ARIES (sheep) / Organ: BRAIN / References: UniProt: D0VWZ0
#2: Protein Tubulin beta chain


Mass: 50043.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) OVIS ARIES (sheep) / Organ: BRAIN / References: UniProt: D0VWY9
#3: Protein Stathmin-like domain R1


Mass: 10117.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artificial gene (others) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Protein Designed ankyrin repeat protein (DARPIN) D2


Mass: 18140.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artificial gene (others) / Plasmid: PDST067 (PQE30 DERIVATIVE) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE

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Non-polymers , 6 types, 107 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHOR STATES THAT THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT BECAUSE THE SEQUENCE ...AUTHOR STATES THAT THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT BECAUSE THE SEQUENCE OF OVINE BRAIN TUBULIN IS NOT AVAILABLE. FOR ALPHA-TUBULIN (CHAIN A) THEY USED THE ALPHA 1B ISOTYPE SEQUENCE (NCBI NP_001108328.1). FOR BETA-TUBULIN (CHAIN B), THERE ARE THREE MAJOR ISOTYPES EXPRESSED IN THE BRAIN. THEY USED MAINLY THE BETA 2B ISOTYPE SEQUENCE (NCBI NP_001003900.1) BUT INTRODUCED POINT MUTATIONS WHEN POSSIBLE TO TAKE INTO ACCOUNT THE ISOTYPE DIVERSITY.

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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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG, MES BUFFER, PH 6.5, 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: 0.979 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.64→48.55 Å / Num. obs: 32036 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 69.33 Å2 / Rsym value: 0.089 / Net I/σ(I): 10.5
Reflection shellResolution: 2.64→2.78 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.627 / % possible all: 97.5

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Processing

Software
NameVersionClassification
AMoREphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RYC, 2XEE

3ryc

2xee


Resolution: 2.64→45.45 Å / Cor.coef. Fo:Fc: 0.9427 / Cor.coef. Fo:Fc free: 0.9329 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 1617 5.06 %RANDOM
Rwork0.1766 ---
obs0.1778 31979 98.61 %-
Displacement parametersBiso mean: 60.09 Å2
Baniso -1Baniso -2Baniso -3
1-5.622 Å20 Å22.2866 Å2
2---12.0293 Å20 Å2
3---6.4073 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.64→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8446 0 78 102 8626
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018697HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.211800HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3010SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes235HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1288HARMONIC5
X-RAY DIFFRACTIONt_it8697HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion20.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1141SEMIHARMONIC5
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_contact9975SEMIHARMONIC4
LS refinement shellResolution: 2.64→2.73 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2786 151 5.24 %
Rwork0.2141 2732 -
all0.2175 2883 -
obs--98.61 %
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)
10.9385-0.31520.27481.8435-1.10141.90850.02590.0681-0.1316-0.03470.0061-0.08430.2016-0.0184-0.032-0.2960.0096-0.0018-0.2508-0.046-0.300140.4507-18.195358.3309
20.80540.06910.03571.1215-0.56770.89160.00740.02590.018-0.0775-0.00820.00550.0844-0.07790.0008-0.2403-0.00080.0124-0.1753-0.0137-0.209830.64536.833726.3682
31.50380.088-0.69722.76091.40043.34380.03140.08340.0786-0.0025-0.0906-0.1031-0.2065-0.24290.0593-0.30390.0409-0.0122-0.25130.0342-0.179933.861231.63030.6709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|437 A|501 - A|502 C|12 - C|62 }A1 - 437
2X-RAY DIFFRACTION1{ A|1 - A|437 A|501 - A|502 C|12 - C|62 }A501 - 502
3X-RAY DIFFRACTION1{ A|1 - A|437 A|501 - A|502 C|12 - C|62 }C12 - 62
4X-RAY DIFFRACTION2{ C|63 - C|90 B|1 - B|441 B|501 - B|501 }C63 - 90
5X-RAY DIFFRACTION2{ C|63 - C|90 B|1 - B|441 B|501 - B|501 }B1 - 441
6X-RAY DIFFRACTION2{ C|63 - C|90 B|1 - B|441 B|501 - B|501 }B501
7X-RAY DIFFRACTION3{ D|11 - D|169 }D11 - 169

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