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

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Basic information

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 / homology
Function and homology information


positive regulation of axon guidance / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle ...positive regulation of axon guidance / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nervous system development / microtubule / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / GTP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase 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 ...Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase 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 / 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 / TAXOL / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 3.5 Å
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.
History
DepositionJun 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 11, 2014Group: Database references / Derived calculations
Revision 1.4Oct 4, 2017Group: Data collection / Data processing / Refinement description
Category: em_3d_reconstruction / em_image_scans / software
Revision 1.5Aug 16, 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_ref_seq / 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.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_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Polymers100,0152
Non-polymers1,9105
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-62 kcal/mol
Surface area29840 Å2
MethodPISA
Unit cell
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-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein tubulin alpha chain


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


Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / 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 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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-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
#7: Chemical ChemComp-TA1 / TAXOL / Paclitaxel


Mass: 853.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM

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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 / 3D 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 growTemperature: 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 modeModelModeSpecimen-ID
1SPOT SCANJEOL 4000BRIGHT FIELDBright-field microscopy1
2FLOOD BEAMJEOL 4000DIFFRACTION1
Image recordingFilm or detector model: GENERIC FILM / Details: low dose
Diffraction
IDMean temperature (K)Crystal-ID
1931
21
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: JEOL 4000 electron microscope / Wavelength: 0.0194 Å
Detector
TypeIDDetectorDate
KODAK1FILMJan 1, 1994
GATAN2CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0194 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. all: 12422 / Num. obs: 12422 / % possible obs: 73 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.25 / Net I/σ(I): 5.4
Reflection shellResolution: 3.5→3.7 Å / Mean I/σ(I) obs: 2.3 / Num. unique all: 1080 / % possible all: 73
Reflection
*PLUS
% possible obs: 73 %

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Processing

Software
NameVersionClassification
CCP4model building
CNS0.9refinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TUB

1tub


Resolution: 3.5→20 Å / Isotropic thermal model: overall anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber / Details: constrained
RfactorNum. reflectionSelection details
Rfree0.2966 623 random
Rwork0.2315 --
all-12422 -
obs-12422 -
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1-26.5 Å20 Å20 Å2
2--10.8 Å20 Å2
3----37.4 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 124 0 6702
Refine LS restraints
Refine-IDTypeDev ideal
ELECTRON CRYSTALLOGRAPHYc_bond_d0.01
ELECTRON CRYSTALLOGRAPHYc_angle_d1.561
LS refinement shellResolution: 3.5→3.66 Å
RfactorNum. reflection
Rfree0.3834 58
Rwork0.2315 -
obs-1080
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.4 Å2
LS refinement shell
*PLUS
Highest resolution: 3.5 Å

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