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- PDB-7f1b: Odinarchaeota tubulin H393D mutant, in a pseudo protofilament arr... -

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Basic information

Entry
Database: PDB / ID: 7f1b
TitleOdinarchaeota tubulin H393D mutant, in a pseudo protofilament arrangement, after GTP hydrolysis and phosphate release
ComponentsTubulin-like protein
KeywordsSTRUCTURAL PROTEIN / Asgard / tubulin / GTP / filament
Function / homology
Function and homology information


microtubule-based process / structural constituent of cytoskeleton / microtubule / GTPase activity / GTP binding
Similarity search - Function
Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain ...Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / 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
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Tubulin-like protein CetZ
Similarity search - Component
Biological speciesOdinarchaeota archaeon
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRobinson, R.C. / Akil, C. / Tran, L.T.
Funding support Japan, United States, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR19S5 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00476 Japan
Other privateMoore Simons Foundation GBMF9743 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution.
Authors: Caner Akıl / Samson Ali / Linh T Tran / Jérémie Gaillard / Wenfei Li / Kenichi Hayashida / Mika Hirose / Takayuki Kato / Atsunori Oshima / Kosuke Fujishima / Laurent Blanchoin / Akihiro ...Authors: Caner Akıl / Samson Ali / Linh T Tran / Jérémie Gaillard / Wenfei Li / Kenichi Hayashida / Mika Hirose / Takayuki Kato / Atsunori Oshima / Kosuke Fujishima / Laurent Blanchoin / Akihiro Narita / Robert C Robinson /
Abstract: Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic ...Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound x-ray structures of an Asgard tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the "+" end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolutionary stage intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.
History
DepositionJun 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tubulin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1013
Polymers47,6331
Non-polymers4682
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-14 kcal/mol
Surface area16860 Å2
Unit cell
Length a, b, c (Å)40.883, 94.428, 100.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tubulin-like protein


Mass: 47633.406 Da / Num. of mol.: 1 / Mutation: H393D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Odinarchaeota archaeon (strain LCB_4) (archaea)
Strain: LCB_4 / Gene: cetZ, OdinLCB4_01330 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9N9N5
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% PEG 1500 0.1 M MMT (1 DL-malic acid: 2 MES: 2 Tris base), pH 9.0 soak: 10 mM GTP (1 h) then no GTP (14 days) 1 mM MgCl2, 0.1 M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→29.55 Å / Num. obs: 15927 / % possible obs: 99.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.035 / Rrim(I) all: 0.123 / Net I/σ(I): 13.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.605 / Num. unique obs: 1616 / CC1/2: 0.912 / R split: 2.5 / Rpim(I) all: 0.252 / Rrim(I) all: 0.657 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIXv1.17.1refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EVH

7evh


Resolution: 2.4→29.55 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 786 -
Rwork0.2079 --
obs-15867 99.81 %
Displacement parametersBiso mean: 68.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 29 32 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00173371
X-RAY DIFFRACTIONf_angle_d0.49744569
X-RAY DIFFRACTIONf_chiral_restr0.0407519
X-RAY DIFFRACTIONf_plane_restr0.0031582
X-RAY DIFFRACTIONf_dihedral_angle_d16.81651245
LS refinement shellResolution: 2.4→2.486 Å
RfactorNum. reflection% reflection
Rfree0.3827 75 -
Rwork0.2809 711 -
obs--99.74 %
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)
11.98-1.2752-0.03361.4974-0.71072.99880.08240.31040.0258-0.1480.0421-0.17360.3360.767400.56950.0986-0.08210.6371-0.12840.536831.710953.423316.2146
24.0528-1.1426-0.31492.70470.59655.159-0.0054-0.3007-0.14560.27850.2120.10910.55560.08480.00130.47450.0259-0.09720.33820.04120.490126.033451.989141.9362
32.4649-0.75570.19052.2524-0.08364.88490.16620.24940.21470.07050.0015-0.01050.0396-0.1109-00.39040.0141-0.01920.4687-0.01430.450922.971758.84829.2023
42.0832-0.3284-0.66120.68510.40944.01090.1409-0.01341.0611-0.37560.1842-0.0645-2.7861-0.11180.02461.1174-0.00730.04140.5287-0.01910.78319.836673.018826.3353
50.4010.2436-0.44020.9594-0.42760.97260.0206-0.2960.17470.2515-0.27120.3226-1.7724-2.0374-0.0040.85240.3971-0.01491.27710.0480.75558.307469.108426.1393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 359 through 423 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 264 )
4X-RAY DIFFRACTION4chain 'A' and (resid 265 through 305 )
5X-RAY DIFFRACTION5chain 'A' and (resid 306 through 358 )

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