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- PDB-9f07: TUBULIN:STATHMIN:DARPIN:TAU MTBR3 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 9f07
TitleTUBULIN:STATHMIN:DARPIN:TAU MTBR3 COMPLEX
Components
  • D2-R3
  • Stathmin-4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / MICROTUBULE TAU FUSION PROTEIN
Function / homology
Function and homology information


organelle transport along microtubule / axonemal microtubule / forebrain morphogenesis / glial cell differentiation / neuron projection arborization / cerebellar cortex morphogenesis / flagellated sperm motility / dentate gyrus development / centrosome cycle / microtubule depolymerization ...organelle transport along microtubule / axonemal microtubule / forebrain morphogenesis / glial cell differentiation / neuron projection arborization / cerebellar cortex morphogenesis / flagellated sperm motility / dentate gyrus development / centrosome cycle / microtubule depolymerization / pyramidal neuron differentiation / motor behavior / smoothened signaling pathway / response to L-glutamate / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / sperm flagellum / response to tumor necrosis factor / regulation of microtubule polymerization or depolymerization / microtubule-based process / response to mechanical stimulus / condensed chromosome / homeostasis of number of cells within a tissue / tubulin binding / cellular response to calcium ion / adult locomotory behavior / intracellular protein transport / synapse organization / neuromuscular junction / visual learning / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / cytoplasmic ribonucleoprotein granule / neuron migration / neuron projection development / growth cone / neuron apoptotic process / gene expression / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / metal ion binding / identical protein binding / plasma membrane / cytosol / 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Tubulin beta chain / Tubulin alpha chain / Stathmin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.211 Å
AuthorsAmmar Khodja, L. / Campanacci, V. / Gigant, b.
Funding support France, 3items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)MITI France
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0002-01 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
CitationJournal: Pnas Nexus / Year: 2024
Title: The structure of a Tau fragment bound to tubulin prompts new hypotheses on Tau mechanism and oligomerization.
Authors: Ammar Khodja, L. / Campanacci, V. / Lippens, G. / Gigant, B.
History
DepositionApr 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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-4
D: D2-R3
E: Tubulin alpha chain
F: Tubulin beta chain
G: Stathmin-4
H: D2-R3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,16830
Polymers266,0588
Non-polymers4,11022
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29470 Å2
ΔGint-104 kcal/mol
Surface area78500 Å2
Unit cell
Length a, b, c (Å)52.298, 222.25, 227.657
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#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: 49999.887 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 / SLD1-R3


Mass: 13157.819 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STMN4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H169
#4: Protein D2-R3


Mass: 19666.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 9 types, 350 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: 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
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#11: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#12: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20 to 25% (w/v) polyethylene glycol 3350 0.2 M K/Na tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.211→159.032 Å / Num. obs: 81231 / % possible obs: 60.6 % / Redundancy: 27.4 % / CC1/2: 0.996 / Rpim(I) all: 0.082 / Net I/σ(I): 9.4
Reflection shellResolution: 2.211→2.511 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4062 / CC1/2: 0.607 / Rpim(I) all: 0.798

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.211→159.03 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.642 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.636 / SU Rfree Blow DPI: 0.277 / SU Rfree Cruickshank DPI: 0.282
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 4073 -RANDOM
Rwork0.1997 ---
obs0.2014 81231 60.6 %-
Displacement parametersBiso mean: 44.79 Å2
Baniso -1Baniso -2Baniso -3
1--7.4174 Å20 Å20 Å2
2--5.0927 Å20 Å2
3---2.3247 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.211→159.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16810 0 263 328 17401
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00817457HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9323649HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6045SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3006HARMONIC5
X-RAY DIFFRACTIONt_it17320HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2285SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact14326SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion19.44
LS refinement shellResolution: 2.211→2.39 Å
RfactorNum. reflection% reflection
Rfree0.2778 80 -
Rwork0.2845 --
obs--5.86 %
Refinement TLS params.

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)
11.4861-0.27880.10416.01660.59821.14970.0674-0.3850.2269-0.385-0.12-0.10920.2269-0.10920.0526-0.0872-0.0482-0.0197-0.0581-0.07410.298225.4395-33.0812-96.9439
21.5285-0.1242-0.04271.74430.48551.20570.0139-0.0222-0.0442-0.0222-0.0388-0.0659-0.0442-0.06590.0249-0.23570.0039-0.0069-0.0311-0.0145-0.131123.3659.4505-91.1974
33.91840.21-1.5015.66890.86648.6726-0.1574-0.8801-1.1191-0.8801-0.09250.0844-1.11910.08440.24990.1652-0.0239-0.0939-0.1922-0.0461-0.205533.122942.1721-82.176
41.48660.29040.08953.3439-0.82141.69690.0582-0.0310.4385-0.0310.02420.09770.43850.0977-0.0823-0.19410.0546-0.0298-0.1493-0.0170.0319-14.818-28.55-20.587
51.32440.0001-0.05891.5395-0.5741.5732-0.0140.006-0.03760.006-0.04230.1084-0.03760.10840.0563-0.2660.0108-0.00840.01130.0057-0.1489-12.492213.1397-31.507
63.2671-1.0533-1.76244.0498-0.14629.5496-0.30780.759-1.30720.7590.022-0.0118-1.3072-0.01180.28590.07940.0504-0.1126-0.15390.008-0.2817-23.200644.2379-44.0421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|604 C|205 - C|265 }A1 - 439
2X-RAY DIFFRACTION1{ A|1 - A|604 C|205 - C|265 }A501 - 502
3X-RAY DIFFRACTION1{ A|1 - A|604 C|205 - C|265 }A601 - 604
4X-RAY DIFFRACTION1{ A|1 - A|604 C|205 - C|265 }C205 - 265
5X-RAY DIFFRACTION2{ B|1 - B|501 C|266 - C|291 }B1 - 441
6X-RAY DIFFRACTION2{ B|1 - B|501 C|266 - C|291 }B501
7X-RAY DIFFRACTION2{ B|1 - B|501 C|266 - C|291 }C266 - 291
8X-RAY DIFFRACTION3{ D|147 - D|292 }D147 - 292
9X-RAY DIFFRACTION4{ E|1 - E|604 G|207 - G|265 }E1 - 437
10X-RAY DIFFRACTION4{ E|1 - E|604 G|207 - G|265 }E501 - 502
11X-RAY DIFFRACTION4{ E|1 - E|604 G|207 - G|265 }E601 - 604
12X-RAY DIFFRACTION4{ E|1 - E|604 G|207 - G|265 }G207 - 265
13X-RAY DIFFRACTION5{ F|1 - F|501 G|266 - G|316 D|305 - D|313 }D305 - 313
14X-RAY DIFFRACTION5{ F|1 - F|501 G|266 - G|316 D|305 - D|313 }F1 - 441
15X-RAY DIFFRACTION5{ F|1 - F|501 G|266 - G|316 D|305 - D|313 }F501
16X-RAY DIFFRACTION5{ F|1 - F|501 G|266 - G|316 D|305 - D|313 }G266 - 316
17X-RAY DIFFRACTION6{ H|* }H147 - 292
18X-RAY DIFFRACTION6{ H|* }H335

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