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- PDB-6gwc: Tubulin:iE5 alphaRep complex -

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Basic information

Entry
Database: PDB / ID: 6gwc
TitleTubulin:iE5 alphaRep complex
Components
  • ALPHA-TUBULIN
  • Tubulin beta chain
  • iE5 ALPHAREP
KeywordsCELL CYCLE / microtubule / ARTIFICIAL PROTEIN / ALPHAREP / cytoskeleton
Function / homology
Function and homology information


microtubule-based process / structural constituent of cytoskeleton / microtubule / GTPase activity / GTP binding / 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. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain ...Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / 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 / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / TRIETHYLENE GLYCOL / Tubulin beta chain
Similarity search - Component
Biological speciessynthetic construct (others)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGigant, B. / Campanacci, V.
CitationJournal: Structure / Year: 2019
Title: Selection and Characterization of Artificial Proteins Targeting the Tubulin alpha Subunit.
Authors: Campanacci, V. / Urvoas, A. / Consolati, T. / Cantos-Fernandes, S. / Aumont-Nicaise, M. / Valerio-Lepiniec, M. / Surrey, T. / Minard, P. / Gigant, B.
History
DepositionJun 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: 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
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-TUBULIN
B: Tubulin beta chain
C: iE5 ALPHAREP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,01410
Polymers125,3783
Non-polymers1,6367
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-32 kcal/mol
Surface area38580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.346, 102.346, 216.207
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein ALPHA-TUBULIN


Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9
#3: Protein iE5 ALPHAREP


Mass: 25173.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 183 molecules

#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 52.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 13% polyethylene glycol 400, 0.1 M Mes-K pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.6→46.25 Å / Num. obs: 41238 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 80.08 Å2 / Net I/σ(I): 14.6
Reflection shellResolution: 2.6→2.69 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DRX, 3LTJ

4drx

3ltj


Resolution: 2.6→46.25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.491 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.5 / SU Rfree Blow DPI: 0.26 / SU Rfree Cruickshank DPI: 0.262
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2062 5 %RANDOM
Rwork0.173 ---
obs0.176 41238 100 %-
Displacement parametersBiso mean: 70.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.1073 Å20 Å20 Å2
2---1.1073 Å20 Å2
3---2.2145 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.6→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8202 0 100 176 8478
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018527HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1611641HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2929SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1490HARMONIC5
X-RAY DIFFRACTIONt_it8527HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion21.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1118SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9848SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.62 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3689 -4.97 %
Rwork0.3254 784 -
all0.3273 825 -
obs--98.7 %
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)
11.6397-0.3466-0.59370.7512-0.07781.50820.0195-0.132-0.0244-0.0441-0.0585-0.0339-0.05980.19710.03890.2086-0.09710.07180.21230.01440.235270.1444-12.1967-29.3836
22.1430.1747-1.41421.8765-0.01643.65080.1488-0.3393-0.03910.3711-0.0843-0.05490.09-0.1648-0.06450.2603-0.12970.06210.2490.03090.185537.4816-12.7458-1.927
33.7774-0.1772-0.61850.8592-0.0011.85020.17720.15890.2586-0.1173-0.0058-0.1621-0.40240.2106-0.1715-0.1148-0.18660.1091-0.13440.0136-0.184790.1547-4.0856-52.5476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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