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- PDB-1jff: Refined structure of alpha-beta tubulin from zinc-induced sheets ... -

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Entry
Database: PDB / ID: 1jff
TitleRefined structure of alpha-beta tubulin from zinc-induced sheets stabilized with taxol
Components
  • tubulin alpha chain
  • tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / dimer / GTPase
Function / homologyTubulin/FtsZ, GTPase domain superfamily / Tubulin C-terminal domain / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, C-terminal / Cilium Assembly / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ family, GTPase domain / Tubulin subunits alpha, beta, and gamma signature. ...Tubulin/FtsZ, GTPase domain superfamily / Tubulin C-terminal domain / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, C-terminal / Cilium Assembly / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ family, GTPase domain / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ, GTPase domain / Tubulin-beta mRNA autoregulation signal. / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / MHC class II antigen presentation / Separation of Sister Chromatids / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Recruitment of NuMA to mitotic centrosomes / Tubulin/FtsZ, C-terminal / Beta tubulin / Hedgehog 'off' state / COPI-mediated anterograde transport / Kinesins / Carboxyterminal post-translational modifications of tubulin / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Recycling pathway of L1 / Alpha tubulin / RHO GTPases Activate Formins / RHO GTPases activate IQGAPs / Intraflagellar transport / Tubulin / positive regulation of axon guidance / cytoplasmic microtubule / cellular response to interleukin-4 / microtubule-based process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / microtubule / GTPase activity / GTP binding / ubiquitin protein ligase binding / protein heterodimerization activity / cytosol / cytoplasm / Tubulin alpha-1B chain / Tubulin beta-2B chain
Function and homology information
Specimen sourceBos taurus (cattle)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / 3.5 Å resolution
AuthorsLowe, J. / Li, H. / Downing, K.H. / Nogales, E.
Citation
Journal: J. Mol. Biol. / Year: 2001
Title: Refined structure of alpha beta-tubulin at 3.5 A resolution.
Authors: J Löwe / H Li / K H Downing / E Nogales
Abstract: We present a refined model of the alpha beta-tubulin dimer to 3.5 A resolution. An improved experimental density for the zinc-induced tubulin sheets was obtained by adding 114 electron diffraction ...We present a refined model of the alpha beta-tubulin dimer to 3.5 A resolution. An improved experimental density for the zinc-induced tubulin sheets was obtained by adding 114 electron diffraction patterns at 40-60 degrees tilt and increasing the completeness of structure factor amplitudes to 84.7 %. The refined structure was obtained using maximum-likelihood including phase information from experimental images, and simulated annealing Cartesian refinement to an R-factor of 23.2 and free R-factor of 29.7. The current model includes residues alpha:2-34, alpha:61-439, beta:2-437, one molecule of GTP, one of GDP, and one of taxol, as well as one magnesium ion at the non-exchangeable nucleotide site, and one putative zinc ion near the M-loop in the alpha-tubulin subunit. The acidic C-terminal tails could not be traced accurately, neither could the N-terminal loop including residues 35-60 in the alpha-subunit. There are no major changes in the overall fold of tubulin with respect to the previous structure, testifying to the quality of the initial experimental phases. The overall geometry of the model is, however, greatly improved, and the position of side-chains, especially those of exposed polar/charged groups, is much better defined. Three short protein sequence frame shifts were detected with respect to the non-refined structure. In light of the new model we discuss details of the tubulin structure such as nucleotide and taxol binding sites, lateral contacts in zinc-sheets, and the significance of the location of highly conserved residues.
#1: Journal: Nature / Year: 1998
Title: Structure of the alpha beta tubulin dimer by electron crystallography
Authors: Nogales, E. / Wolf, S.G. / Downing, K.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 20, 2001 / Release: Sep 19, 2001
RevisionDateData content typeGroupCategoryProviderType
1.0Sep 19, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jun 11, 2014Structure modelDatabase references / Derived calculations
1.4Oct 4, 2017Structure modelData collection / Data processing / Refinement descriptionem_3d_reconstruction / em_image_scans / software

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Structure visualization

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Assembly

Deposited unit
A: tubulin alpha chain
B: tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9257
Polyers100,0152
Non-polymers1,9105
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)6790
ΔGint (kcal/M)-62
Surface area (Å2)29840
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)81.200, 93.500, 90.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Protein/peptide , 2 types, 2 molecules AB

#1: Protein/peptide tubulin alpha chain


Mass: 50107.238 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: Brain / References: UniProt: P81947*PLUS
#2: Protein/peptide tubulin beta chain


Mass: 49907.770 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: Brain / References: UniProt: Q6B856*PLUS

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Non-polymers , 5 types, 5 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM
#7: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Formula: C47H51NO14 / Paclitaxel

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Details

Sequence detailsTHE SAMPLE WAS BOVINE, BUT THE MODELED PROTEIN SEQUENCES ARE FROM SUS SCROFA (PIG). THE AUTHORS ...THE SAMPLE WAS BOVINE, BUT THE MODELED PROTEIN SEQUENCES ARE FROM SUS SCROFA (PIG). THE AUTHORS USED THE SEQUENCES FROM THE MOST ABUNDANT ISOTYPE OF PIG BRAIN TUBULIN. THE RESIDUES IN CHAIN B ARE NOT SEQUENTIALLY NUMBERED. RESIDUES 44 AND 47 AND RESIDUES 360 AND 369 ARE COVALENTLY BOUND.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 200
EM experimentAggregation state: 2D ARRAY / Reconstruction method: electron crystallography

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Sample preparation

ComponentName: Alpha-Beta-tubulin sheets / Type: COMPLEX
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: tannin
VitrificationCryogen name: NITROGEN
CrystalDescription: JEOL 4000 electron microscope was used. Kodak film and gatan CCD were used as detectors. Temperature was 93 Kelvin.
Crystal growTemp: 305 K / Method: aberrant polymerization of tubulin / pH: 5.8
Details: Zn++, pH 5.8, aberrant polymerization of tubulin, temperature 305K
Crystal grow
*PLUS
Method: unknown

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Data collection

EM imaging
IDIllumination modeMicroscope modelModeSpecimen ID
1SPOT SCANJEOL 4000BRIGHT FIELD1
2FLOOD BEAMJEOL 4000DIFFRACTION1
Image recordingDetails: low dose / Film or detector model: GENERIC FILM
Diffraction
IDMean temperatureCrystal ID
1931
21
SourceSource: ELECTRON MICROSCOPE / Type: JEOL 4000 electron microscope / Wavelength: 0.0194 Å
Detector
TypeIdDetectorCollection date
KODAK1FILM1994-01-01
GATAN2CCD
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: electron
Radiation wavelengthWavelength: 0.0194 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 40 Å2 / D resolution high: 3.5 Å / D resolution low: 2 Å / Number all: 12422 / Number obs: 12422 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.25 / NetI over sigmaI: 5.4 / Redundancy: 6 % / Percent possible obs: 73
Reflection shellHighest resolution: 3.5 Å / Lowest resolution: 3.7 Å / MeanI over sigI obs: 2.3 / Number unique all: 1080 / Percent possible all: 73
Reflection
*PLUS
Percent possible obs: 73

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Processing

Software
NameVersionClassification
CCP4model building
CNS0.9refinement
CCP4phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TUB
Details: constrained / R Free selection details: random / Isotropic thermal model: overall anisotropic / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh and Huber
Displacement parametersB iso mean: 41.4 Å2 / Aniso B11: 26.5 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 10.8 Å2 / Aniso B23: 0 Å2 / Aniso B33: -37.4 Å2
Least-squares processR factor R free: 0.2966 / R factor R work: 0.2315 / Highest resolution: 3.5 Å / Lowest resolution: 20 Å / Number reflection R free: 623 / Number reflection all: 12422 / Number reflection obs: 12422
Refine hist #LASTHighest resolution: 3.5 Å / Lowest resolution: 20 Å
Number of atoms included #LASTProtein: 6578 / Nucleic acid: 0 / Ligand: 124 / Solvent: 0 / Total: 6702
Refine LS restraints
Refine IDTypeDev ideal
ELECTRON CRYSTALLOGRAPHYc_bond_d0.010
ELECTRON CRYSTALLOGRAPHYc_angle_d1.561
Refine LS shellHighest resolution: 3.5 Å / R factor R free: 0.3834 / R factor R work: 0.2315 / Lowest resolution: 3.66 Å / Number reflection R free: 58 / Number reflection obs: 1080
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine
*PLUS
Sigma F: 0
Displacement parameters
*PLUS
B iso mean: 41.4 Å2
Least-squares process
*PLUS
R factor obs: 0.231 / Highest resolution: 3.5 Å / Lowest resolution: 2 Å
Refine LS shell
*PLUS
Highest resolution: 3.5 Å

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