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- PDB-4ffb: A TOG:alpha/beta-tubulin Complex Structure Reveals Conformation-B... -

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Basic information

Entry
Database: PDB / ID: 4ffb
TitleA TOG:alpha/beta-tubulin Complex Structure Reveals Conformation-Based Mechanisms For a Microtubule Polymerase
Components
  • Protein STU2
  • Tubulin alpha-1 chain
  • Tubulin beta chain
KeywordsHYDROLASE / tubulin fold / HEAT repeats / cytoskeleton / microtubule / tubulin / TOG domain
Function / homology
Function and homology information


microtubule plus end polymerase / nuclear migration by microtubule mediated pushing forces / mitotic sister chromatid biorientation / nuclear division / establishment or maintenance of microtubule cytoskeleton polarity / repair of mitotic kinetochore microtubule attachment defect / mitotic spindle elongation / Platelet degranulation / homologous chromosome segregation / positive regulation of intracellular protein transport ...microtubule plus end polymerase / nuclear migration by microtubule mediated pushing forces / mitotic sister chromatid biorientation / nuclear division / establishment or maintenance of microtubule cytoskeleton polarity / repair of mitotic kinetochore microtubule attachment defect / mitotic spindle elongation / Platelet degranulation / homologous chromosome segregation / positive regulation of intracellular protein transport / nuclear migration along microtubule / microtubule nucleation / microtubule plus-end binding / spindle pole body / tubulin complex / microtubule polymerization / mitotic sister chromatid segregation / mitotic spindle assembly / microtubule-based process / cytoplasmic microtubule organization / cytoskeleton organization / nuclear periphery / mitotic spindle organization / spindle microtubule / kinetochore / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / spindle pole / mitotic cell cycle / cell cortex / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / response to antibiotic / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / Stu2, C-terminal segment / XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / TOG domain / TOG / Helix hairpin bin / HEAT repeat profile. / HEAT, type 2 ...: / Stu2, C-terminal segment / XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / TOG domain / TOG / Helix hairpin bin / HEAT repeat profile. / HEAT, type 2 / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 / Armadillo-like helical / Helix Hairpins / Alpha Horseshoe / Armadillo-type fold / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha-1 chain / Protein STU2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.882 Å
AuthorsAyaz, P. / Ye, X. / Huddleston, P. / Brautigam, C.A. / Rice, L.M.
CitationJournal: Science / Year: 2012
Title: A TOG: alpha beta-tubulin complex structure reveals conformation-based mechanisms for a microtubule polymerase.
Authors: Ayaz, P. / Ye, X. / Huddleston, P. / Brautigam, C.A. / Rice, L.M.
History
DepositionMay 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: 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_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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_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-1 chain
B: Tubulin beta chain
C: Protein STU2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,5267
Polymers133,4313
Non-polymers1,0954
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.120, 98.040, 91.366
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tubulin alpha-1 chain


Mass: 49853.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TUB1, YML085C / Plasmid: p426Gal1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): JEL1 / References: UniProt: P09733
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 51910.477 Da / Num. of mol.: 1 / Mutation: T175R,V179R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TUB2, YFL037W / Plasmid: p424Gal1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): JEL1 / References: UniProt: P02557, EC: 3.6.5.6
#3: Protein Protein STU2 / Suppressor of tubulin 2


Mass: 31666.191 Da / Num. of mol.: 1 / Fragment: TOG1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: L2108, STU2, YLR045C / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46675
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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

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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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 20% (v/v) PEG 400, 0.1 M MES pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. all: 39347 / Num. obs: 39347 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.88→2.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 0.9 / % possible all: 22.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1063)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SA0 CHAIN A, 1SA0 CHAIN B, 2QK1

1sa0

1sa0

2qk1


Resolution: 2.882→44.945 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 29.61 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 1039 3.97 %random
Rwork0.2075 ---
obs0.2099 26174 74.58 %-
all-27213 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.882→44.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8469 0 66 0 8535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038706
X-RAY DIFFRACTIONf_angle_d0.69711815
X-RAY DIFFRACTIONf_dihedral_angle_d16.843171
X-RAY DIFFRACTIONf_chiral_restr0.0491322
X-RAY DIFFRACTIONf_plane_restr0.0031525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.882-3.03390.3613430.2461082X-RAY DIFFRACTION23
3.0339-3.22390.2837910.2532176X-RAY DIFFRACTION46
3.2239-3.47280.29961270.23733091X-RAY DIFFRACTION65
3.4728-3.82210.28541770.22624257X-RAY DIFFRACTION89
3.8221-4.37470.27181950.19244789X-RAY DIFFRACTION100
4.3747-5.51010.26532020.18594849X-RAY DIFFRACTION100
5.5101-44.95080.23662040.20644891X-RAY DIFFRACTION100
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)
10.2492-0.3452-0.07640.9494-0.06961.7955-0.0104-0.12990.2589-0.03610.116-0.2916-0.53860.3524-0.00020.5788-0.09410.07760.3592-0.07080.413837.83311.513349.1908
22.55070.84560.30242.07310.26971.08990.0390.0330.2365-0.06050.01310.1521-0.14090.12380.00010.40060.00920.08170.28120.04070.326128.37123.978739.1497
32.2868-0.30910.0112.20240.78380.78750.0093-0.3564-0.05440.00790.1233-0.40830.13720.500800.3837-0.0345-0.03670.4626-0.01080.632545.1191-7.091643.991
43.90170.37330.96481.75850.78211.95950.22480.1843-0.39930.10030.0059-0.40490.3040.42490.00050.46210.01320.02430.28560.05730.417238.6437-11.594837.1867
50.5761-0.12140.13381.1586-0.81391.4738-0.0238-0.35870.56770.71930.15330.3298-1.2101-0.37950.03450.67940.17060.12330.7070.06170.7485-4.96875.491350.5561
63.0701-0.3858-0.12581.53880.14792.4291-0.087-0.0560.15290.11240.22590.4545-0.2335-0.81490.00190.42380.11990.04020.6940.21550.646-13.556-2.262238.352
71.56310.0454-0.19351.06520.2841.2720.0426-0.3745-0.34490.31360.17790.3872-0.0775-0.5329-0.0030.46910.00530.00710.50840.15280.53971.988-13.728145.4075
80.6018-0.3267-0.21680.5336-0.52691.39480.2117-0.6009-0.58920.28970.1874-0.17310.5856-0.550.04560.53140.0090.01530.67320.16550.60756.3695-19.695147.2377
92.8673-0.56630.58711.66650.02612.03590.09730.2163-0.483-0.16910.21550.34630.1115-0.61170.00130.4576-0.08260.0030.52050.16470.6653-6.2335-17.009831.2013
100.0332-0.04730.01290.0865-0.03650.0175-0.4011-0.0930.172-0.0452-0.28130.424-0.41630.0389-0.00260.940.2734-0.06911.24630.42021.0412-32.228914.347613.0115
110.60380.3619-0.57641.4682-1.65823.6626-0.73240.273-0.0382-0.3950.35610.5083-0.06-0.7372-0.51180.47450.1078-0.24861.43380.48240.9299-26.95937.03377.4176
120.3844-0.1286-0.21510.35480.20890.1998-0.1114-0.00560.3647-0.2338-0.34110.6669-0.4094-0.6556-0.15140.81760.1731-0.23121.11420.48370.8948-16.173314.37864.7587
130.14890.0351-0.03910.10150.0970.1874-0.22030.46510.2709-0.3679-0.1930.1563-0.510.0199-0.70620.46420.1836-0.30.95710.68050.4566-9.56715.0936.7745
140.54030.23650.05910.4511-0.19560.1544-0.08720.64350.5844-0.2328-0.07190.1969-0.1902-0.082-0.00190.7230.1305-0.07220.79030.30950.68550.862311.66666.7975
150.70750.24130.0590.15210.26440.67560.19160.7640.4465-0.1277-0.03570.1641-0.370.413-0.00130.6721-0.024-0.07910.91080.32340.64939.75468.62115.363
160.0517-0.0691-0.0320.07590.04020.25280.08250.45980.3235-0.95810.1969-0.32930.21280.50310.02840.83350.03350.02470.92880.26640.718419.84481.69997.235
170.11760.0080.16280.07750.03730.09580.02760.3431-0.20330.28990.16960.5752-0.17950.1572-0.02311.31710.197-0.00320.98920.18050.4273-4.97968.8111-18.0195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:53)
2X-RAY DIFFRACTION2chain 'A' and (resseq 54:244)
3X-RAY DIFFRACTION3chain 'A' and (resseq 245:301)
4X-RAY DIFFRACTION4chain 'A' and (resseq 302:439)
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:62)
6X-RAY DIFFRACTION6chain 'B' and (resseq 63:241)
7X-RAY DIFFRACTION7chain 'B' and (resseq 242:298)
8X-RAY DIFFRACTION8chain 'B' and (resseq 299:336)
9X-RAY DIFFRACTION9chain 'B' and (resseq 337:432)
10X-RAY DIFFRACTION10chain 'C' and (resseq 11:22)
11X-RAY DIFFRACTION11chain 'C' and (resseq 23:38)
12X-RAY DIFFRACTION12chain 'C' and (resseq 39:110)
13X-RAY DIFFRACTION13chain 'C' and (resseq 111:131)
14X-RAY DIFFRACTION14chain 'C' and (resseq 132:169)
15X-RAY DIFFRACTION15chain 'C' and (resseq 170:212)
16X-RAY DIFFRACTION16chain 'C' and (resseq 213:241)
17X-RAY DIFFRACTION17chain 'C' and (resseq 242:272)

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