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- PDB-4u3j: TOG2:alpha/beta-tubulin complex -

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Basic information

Entry
Database: PDB / ID: 4u3j
TitleTOG2:alpha/beta-tubulin complex
Components
  • Protein STU2
  • Tubulin alpha-1 chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN/Protein binding / Complex / STRUCTURAL PROTEIN-Protein binding complex
Function / homology
Function and homology information


repair of mitotic kinetochore microtubule attachment defect / microtubule plus end polymerase / nuclear migration by microtubule mediated pushing forces / Cilium Assembly / mitotic sister chromatid biorientation / nuclear division / establishment or maintenance of microtubule cytoskeleton polarity / Sealing of the nuclear envelope (NE) by ESCRT-III / mitotic spindle elongation / nuclear migration along microtubule ...repair of mitotic kinetochore microtubule attachment defect / microtubule plus end polymerase / nuclear migration by microtubule mediated pushing forces / Cilium Assembly / mitotic sister chromatid biorientation / nuclear division / establishment or maintenance of microtubule cytoskeleton polarity / Sealing of the nuclear envelope (NE) by ESCRT-III / mitotic spindle elongation / nuclear migration along microtubule / homologous chromosome segregation / Platelet degranulation / positive regulation of intracellular protein transport / 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 / Neutrophil degranulation / nuclear periphery / mitotic spindle organization / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / kinetochore / spindle pole / mitotic cell cycle / cell cortex / microtubule binding / 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; / 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 / Armadillo-like helical / Alpha Horseshoe / Helix Hairpins / 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: 2.81 Å
AuthorsAyaz, P. / Rice, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098543 United States
CitationJournal: Elife / Year: 2014
Title: A tethered delivery mechanism explains the catalytic action of a microtubule polymerase.
Authors: Ayaz, P. / Munyoki, S. / Geyer, E.A. / Piedra, F.A. / Vu, E.S. / Bromberg, R. / Otwinowski, Z. / Grishin, N.V. / Brautigam, C.A. / Rice, L.M.
History
DepositionJul 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist / struct_conn
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.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

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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)131,6877
Polymers130,5923
Non-polymers1,0954
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.909, 89.573, 135.508
Angle α, β, γ (deg.)90.00, 112.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABC

#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)
Gene: TUB1 / 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)
Gene: TUB2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): JEL1 / References: UniProt: P02557
#3: Protein Protein STU2 / Suppressor of tubulin 2


Mass: 28827.430 Da / Num. of mol.: 1 / Fragment: TOG2 domain (UNP residues 318-560)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: STU2 / Plasmid: pET-29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46675

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Non-polymers , 3 types, 25 molecules

#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 / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 25% (v/v) PEG3350, 0.25 M (NH4)2SO4, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 26235 / % possible obs: 86.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 9.6
Reflection shellResolution: 2.81→2.92 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.924 / Mean I/σ(I) obs: 1.1 / % possible all: 35.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1627) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FFB,2QK1

4ffb

2qk1


Resolution: 2.81→34.069 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 1305 4.98 %
Rwork0.2176 --
obs0.2197 26230 86.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→34.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8437 0 66 21 8524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038677
X-RAY DIFFRACTIONf_angle_d0.65611784
X-RAY DIFFRACTIONf_dihedral_angle_d15.3353151
X-RAY DIFFRACTIONf_chiral_restr0.0261318
X-RAY DIFFRACTIONf_plane_restr0.0031526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8097-2.92210.4115570.32961145X-RAY DIFFRACTION36
2.9221-3.05510.35481100.31982110X-RAY DIFFRACTION66
3.0551-3.2160.33331460.29932729X-RAY DIFFRACTION85
3.216-3.41730.30881570.26653043X-RAY DIFFRACTION95
3.4173-3.68090.28831720.24183093X-RAY DIFFRACTION98
3.6809-4.05080.25381580.20813178X-RAY DIFFRACTION99
4.0508-4.63570.23051680.17683190X-RAY DIFFRACTION99
4.6357-5.83570.24051650.19373192X-RAY DIFFRACTION99
5.8357-34.07130.19621720.18533245X-RAY DIFFRACTION99
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)
15.1699-1.74430.38991.51381.16252.5875-0.0370.218-0.0825-0.25410.07530.2486-0.482-0.4269-0.00780.39240.113-0.06640.50420.00470.3389-79.2425-12.799129.1083
22.88881.31910.71531.05981.12441.7640.13770.6687-0.0915-0.9382-0.12270.21590.1535-0.2092-0.00010.47990.047-0.02570.49390.00820.3306-64.8881-23.58122.641
34.12870.0185-0.3751.97710.35370.2941-0.00320.28950.3562-0.1175-0.2944-0.2583-0.31440.4087-0.00170.43220.0121-0.0080.2974-0.03150.3911-61.2537-15.563330.885
41.9627-1.01270.53361.86490.37410.14640.0927-0.4198-0.03260.1027-0.16490.2066-0.38040.41440.00160.3399-0.0242-0.05860.3278-0.01490.3519-61.4292-16.691843.9216
51.455-1.1957-0.39841.17570.7430.37160.06070.25190.892-0.38910.10150.3755-0.623-0.36310.00010.60150.0255-0.04030.42930.06850.6213-69.0204-3.380337.432
60.8438-1.13660.61921.72640.16062.32860.1289-0.18790.35910.0757-0.1016-0.0962-0.459-0.07560.00060.3462-0.0328-0.13350.2282-0.03290.5076-62.0233-5.202443.8677
70.16-0.2195-0.0940.35460.13160.083-0.4055-1.33520.0910.4752-0.01190.7012-0.1379-0.213-0.00660.66960.1011-0.01410.4633-0.09880.7202-66.6640.863554.8549
80.184-0.3399-0.18530.47020.24381.22340.43080.1444-0.2493-0.4128-0.5985-0.4852-0.1685-0.06510.0030.5025-0.0659-0.06330.3821-0.00930.613-56.034-4.526951.0968
90.2322-0.17960.49560.2334-0.3290.9233-0.0353-0.01211.5616-1.80890.44830.077-0.01490.15130.00890.4551-0.01580.04220.4603-0.02030.8512-71.06075.563244.8561
100.19070.0555-0.13750.24180.28230.43150.4742-0.43441.27831.1313-0.52910.15660.61381.1087-0.00020.8498-0.0176-0.19770.92430.28721.2371-65.989312.855852.8979
113.6289-3.0739-1.31292.14410.55032.64660.3812-0.61840.7386-0.0668-0.48350.2243-0.37440.1434-0.00460.70010.0656-0.04210.51710.09430.4419-67.53751.388746.0136
120.2866-1.0542-0.26292.66570.051-0.0887-0.6533-0.14780.30461.1470.56750.01240.06070.0972-0.01030.33970.0207-0.03790.4007-0.0060.496-48.4321-19.871446.514
130.41620.0759-0.47561.0350.24661.42560.37860.065-0.0006-0.6246-0.2538-0.2009-0.2212-0.177-0.02270.30030.03830.03030.27230.01560.319-48.6341-33.57433.9468
142.5642-1.56991.1491.1295-0.25881.1325-0.2502-0.26060.5489-0.41770.4735-0.3467-0.51840.66810.00840.3902-0.05770.02780.50860.04380.509-43.6204-14.410839.1329
154.7768-0.559-0.71072.0502-0.58623.1165-0.04460.4135-0.4215-0.147-0.03770.70760.4234-0.6141-0.00070.3997-0.1112-0.02460.4567-0.09190.5469-72.1311-57.201831.7535
162.6517-1.0205-0.24851.68960.66632.8475-0.116-0.0777-0.24240.1595-0.11170.01690.58570.0999-0.00360.42470.01680.03160.30170.00840.4533-59.7548-56.907939.9917
171.62352.5809-0.04333.59260.48533.77220.0339-0.32160.78160.0699-0.14320.44630.0087-0.1646-0.00020.3970.07930.02280.30620.06620.337-61.2038-40.835740.5043
181.9044-0.9954-1.36750.6498-0.25911.9337-0.0573-0.471-0.09080.490.03810.3750.1375-0.1201-0.00040.52650.00690.05510.42990.04190.504-63.8757-41.625255.9078
193.08620.3536-0.79671.444-0.8441.01830.1067-0.2224-0.53510.25930.2083-0.55660.68420.12130.00150.66520.1652-0.06660.43570.09390.5234-44.8403-65.669242.629
200.1303-0.80290.91251.2922-0.31760.7242-0.5388-0.0267-0.14250.62160.7246-0.60710.27320.9653-0.11090.41680.0744-0.0380.67690.09220.4306-41.4218-51.661943.8344
211.2436-1.22660.72372.97360.93022.13750.17190.5326-1.220.0677-0.0597-0.25110.94610.59840.04980.81780.2447-0.00520.7902-0.26240.4548-39.5903-74.56457.3706
221.66650.11560.57314.3644-1.22851.9723-0.16270.569-0.3129-0.45810.1014-0.0213-0.02250.16740.00020.49980.1280.01350.5914-0.09920.3353-41.6341-60.78349.0511
230.2753-0.04520.30875.24811.97872.78640.16090.30470.3646-1.0080.1973-0.1845-0.43630.46160.00940.56350.0140.02750.67660.10260.3746-41.0216-40.5699.0016
240.4790.69670.56811.41251.31141.2723-0.00090.20621.2861-0.86760.2859-0.5893-1.62280.3710.00010.7533-0.0060.16810.74190.12710.7155-37.6049-25.918316.5537
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 183 )
4X-RAY DIFFRACTION4chain 'A' and (resid 184 through 224 )
5X-RAY DIFFRACTION5chain 'A' and (resid 225 through 260 )
6X-RAY DIFFRACTION6chain 'A' and (resid 261 through 280 )
7X-RAY DIFFRACTION7chain 'A' and (resid 288 through 301 )
8X-RAY DIFFRACTION8chain 'A' and (resid 302 through 315 )
9X-RAY DIFFRACTION9chain 'A' and (resid 316 through 325 )
10X-RAY DIFFRACTION10chain 'A' and (resid 326 through 339 )
11X-RAY DIFFRACTION11chain 'A' and (resid 340 through 382 )
12X-RAY DIFFRACTION12chain 'A' and (resid 383 through 402 )
13X-RAY DIFFRACTION13chain 'A' and (resid 403 through 415 )
14X-RAY DIFFRACTION14chain 'A' and (resid 416 through 438 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1 through 126 )
16X-RAY DIFFRACTION16chain 'B' and (resid 127 through 236 )
17X-RAY DIFFRACTION17chain 'B' and (resid 237 through 266 )
18X-RAY DIFFRACTION18chain 'B' and (resid 267 through 371 )
19X-RAY DIFFRACTION19chain 'B' and (resid 372 through 404 )
20X-RAY DIFFRACTION20chain 'B' and (resid 405 through 430 )
21X-RAY DIFFRACTION21chain 'C' and (resid 319 through 369 )
22X-RAY DIFFRACTION22chain 'C' and (resid 370 through 445 )
23X-RAY DIFFRACTION23chain 'C' and (resid 446 through 533 )
24X-RAY DIFFRACTION24chain 'C' and (resid 534 through 559 )

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