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- PDB-4icv: Ubiquitin-like domain of human tubulin folding cofactor E - cryst... -

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Basic information

Entry
Database: PDB / ID: 4icv
TitleUbiquitin-like domain of human tubulin folding cofactor E - crystal form B
ComponentsTubulin-specific chaperone E
KeywordsCHAPERONE / Ubiquitin-like domain / tubulin folding cofactor / alpha tubulin / tubulin folding cofactor B
Function / homology
Function and homology information


peripheral nervous system neuron axonogenesis / post-chaperonin tubulin folding pathway / muscle atrophy / Post-chaperonin tubulin folding pathway / tubulin complex assembly / alpha-tubulin binding / developmental growth / adult locomotory behavior / post-embryonic development / mitotic spindle organization ...peripheral nervous system neuron axonogenesis / post-chaperonin tubulin folding pathway / muscle atrophy / Post-chaperonin tubulin folding pathway / tubulin complex assembly / alpha-tubulin binding / developmental growth / adult locomotory behavior / post-embryonic development / mitotic spindle organization / microtubule cytoskeleton organization / protein folding / protein-folding chaperone binding / microtubule / cytoplasm
Similarity search - Function
Tubulin-specific chaperone E / TBCE, ubiquitin-like (Ubl) domain / Ubiquitin-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Tubulin-specific chaperone E / TBCE, ubiquitin-like (Ubl) domain / Ubiquitin-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Leucine-rich repeat domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
PRASEODYMIUM ION / Tubulin-specific chaperone E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsJanowski, R. / Boutin, M. / Zabala, J.C. / Coll, M.
CitationJournal: J Cell Sci / Year: 2015
Title: The structure of the complex between α-tubulin, TBCE and TBCB reveals a tubulin dimer dissociation mechanism.
Authors: Marina Serna / Gerardo Carranza / Jaime Martín-Benito / Robert Janowski / Albert Canals / Miquel Coll / Juan Carlos Zabala / José María Valpuesta /
Abstract: Tubulin proteostasis is regulated by a group of molecular chaperones termed tubulin cofactors (TBC). Whereas tubulin heterodimer formation is well-characterized biochemically, its dissociation ...Tubulin proteostasis is regulated by a group of molecular chaperones termed tubulin cofactors (TBC). Whereas tubulin heterodimer formation is well-characterized biochemically, its dissociation pathway is not clearly understood. Here, we carried out biochemical assays to dissect the role of the human TBCE and TBCB chaperones in α-tubulin-β-tubulin dissociation. We used electron microscopy and image processing to determine the three-dimensional structure of the human TBCE, TBCB and α-tubulin (αEB) complex, which is formed upon α-tubulin-β-tubulin heterodimer dissociation by the two chaperones. Docking the atomic structures of domains of these proteins, including the TBCE UBL domain, as we determined by X-ray crystallography, allowed description of the molecular architecture of the αEB complex. We found that heterodimer dissociation is an energy-independent process that takes place through a disruption of the α-tubulin-β-tubulin interface that is caused by a steric interaction between β-tubulin and the TBCE cytoskeleton-associated protein glycine-rich (CAP-Gly) and leucine-rich repeat (LRR) domains. The protruding arrangement of chaperone ubiquitin-like (UBL) domains in the αEB complex suggests that there is a direct interaction of this complex with the proteasome, thus mediating α-tubulin degradation.
History
DepositionDec 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: Tubulin-specific chaperone E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2424
Polymers9,8201
Non-polymers4233
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.270, 65.830, 73.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-601-

PR

21A-783-

HOH

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Components

#1: Protein Tubulin-specific chaperone E / Tubulin-folding cofactor E


Mass: 9819.529 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain, UNP residues 443-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBCE / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q15813
#2: Chemical ChemComp-PR / PRASEODYMIUM ION / Praseodymium


Mass: 140.908 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pr
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis Tris pH 6.5 and 43 % (v/v) PEG 400 and 10 mM praseodymium (III) acetate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.4
Reflection shellResolution: 1.45→1.49 Å / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXSphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.789 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18882 903 4.9 %RANDOM
Rwork0.16187 ---
all0.16318 17586 --
obs0.16318 17586 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---0.25 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 3 120 805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022779
X-RAY DIFFRACTIONr_angle_refined_deg1.3242.0261069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17224.85735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26715171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.042156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021577
X-RAY DIFFRACTIONr_mcbond_it1.2771.5460
X-RAY DIFFRACTIONr_mcangle_it2.2522.5764
X-RAY DIFFRACTIONr_scbond_it4.4185319
X-RAY DIFFRACTIONr_scangle_it6.85210292
X-RAY DIFFRACTIONr_rigid_bond_restr1.4813779
LS refinement shellResolution: 1.45→1.528 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.212 134 -
Rwork0.172 2519 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 2.5188 Å / Origin y: 14.2487 Å / Origin z: 24.8838 Å
111213212223313233
T0.014 Å20.0029 Å20.0043 Å2-0.0246 Å20.0182 Å2--0.0256 Å2
L1.8531 °20.1462 °2-0.0381 °2-1.7982 °20.1897 °2--2.0241 °2
S-0.0041 Å °-0.0634 Å °-0.0767 Å °0.087 Å °-0.0196 Å °-0.0593 Å °0.025 Å °0.0338 Å °0.0237 Å °

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