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- PDB-6gwd: Tubulin:iiH5 alphaRep complex -

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Basic information

Entry
Database: PDB / ID: 6gwd
TitleTubulin:iiH5 alphaRep complex
Components
  • ALPHA-TUBULIN
  • Tubulin beta chain
  • iiH5 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'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain
Similarity search - Component
Biological speciessynthetic construct (others)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_label_asym_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: ALPHA-TUBULIN
D: Tubulin beta chain
E: ALPHA-TUBULIN
F: Tubulin beta chain
G: iiH5 ALPHAREP
H: iiH5 ALPHAREP
I: iiH5 ALPHAREP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,18518
Polymers357,2139
Non-polymers2,9729
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19890 Å2
ΔGint-125 kcal/mol
Surface area110560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)450.800, 53.840, 229.620
Angle α, β, γ (deg.)90.00, 118.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 9 molecules ACEBDFGHI

#1: Protein ALPHA-TUBULIN


Mass: 50204.445 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9
#3: Protein iiH5 ALPHAREP


Mass: 18866.582 Da / Num. of mol.: 3
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 , 3 types, 9 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, 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: 3.42 Å3/Da / Density % sol: 64.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.2 M Na tartrate, 12% PEG 3350

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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: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.2→36.85 Å / Num. obs: 80736 / % possible obs: 98.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 117.07 Å2 / Net I/σ(I): 4.17
Reflection shellResolution: 3.2→3.31 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: 3.2→36.85 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.783 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.457
RfactorNum. reflection% reflectionSelection details
Rfree0.27 4034 5 %RANDOM
Rwork0.23 ---
obs0.232 80684 98.7 %-
Displacement parametersBiso mean: 90.62 Å2
Baniso -1Baniso -2Baniso -3
1-10.485 Å20 Å2-13.5676 Å2
2--19.7894 Å20 Å2
3----30.2744 Å2
Refine analyzeLuzzati coordinate error obs: 0.61 Å
Refinement stepCycle: 1 / Resolution: 3.2→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23613 0 183 0 23796
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0124365HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.233132HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8378SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4281HARMONIC5
X-RAY DIFFRACTIONt_it24365HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion22.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3190SEMIHARMONIC5
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_contact27658SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.22 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2492 -5.02 %
Rwork0.2847 1533 -
all0.2829 1614 -
obs--80.35 %
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)
12.24540.2198-1.53013.5535-0.09742.5914-0.0278-0.1321-0.1859-0.2151-0.01910.2015-0.2670.04470.04690.1040.00040.4436-0.50930.04040.2599-80.464-22.383279.3589
22.5243-0.5049-0.93564.67191.18432.7368-0.0904-0.2292-0.05950.56920.2447-0.0117-0.03260.0824-0.15430.12680.08040.5726-0.53530.06750.1184-82.1928-19.4055121.5679
34.28450.1225-0.8382.7684-0.1323-0.22120.0319-0.13120.27050.1987-0.0448-0.0885-0.0091-0.07810.0129-0.00280.04110.382-0.3217-0.01060.2315-104.212-12.859168.7189
44.6376-0.2826-1.33533.41930.42390.648-0.1387-0.04250.12280.42530.07870.29040.08720.16670.06-0.07070.05440.3389-0.3484-0.04170.2185-141.9594-9.7486187.3573
53.1651-0.00391.00660.7259-0.16570.30890.21960.0566-0.05310.14810.0126-0.0437-0.16770.0165-0.23220.0332-0.05040.2028-0.36250.02940.4957-193.146-4.1247188.4524
63.37550.45230.50430.142-0.96890.75770.193-0.0439-0.10690.07640.05020.3692-0.05-0.1359-0.24320.02390.00160.1273-0.4295-0.06570.5825-228.1034-1.1817165.1264
7-3.9572-7.90341.38924.21872.30218.0745-0.13880.833-1.1412-0.46870.1554-1.18910.2521-0.0855-0.0166-0.34830.1202-0.16910.60790.4127-0.8537-66.2119-10.028447.9538
82.1275-0.3407-1.8581.7329-0.39870.6105-0.0003-0.12950.0216-0.0252-0.0741-0.1815-0.16360.10910.07430.0007-0.12060.2766-0.2588-0.06660.3692-70.15720.1679165.2229
91.787-0.83141.5126.01821.34611.2113-0.1281-0.29150.08370.22020.103-0.27120.2316-0.0020.0251-0.0605-0.06460.2306-0.32550.01230.3666-174.0958.3118217.4051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }

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