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- PDB-8oys: De novo designed TIM barrel fold TBF_24 -

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Basic information

Entry
Database: PDB / ID: 8oys
TitleDe novo designed TIM barrel fold TBF_24
ComponentsDe novo designed TIM-barrel
KeywordsDE NOVO PROTEIN / TIM barrel / de novo designed
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsPacesa, M. / Correia, B.E.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
European Research Council (ERC)716058European Union
Citation
Journal: Nature / Year: 2024
Title: Computational design of soluble and functional membrane protein analogues.
Authors: Casper A Goverde / Martin Pacesa / Nicolas Goldbach / Lars J Dornfeld / Petra E M Balbi / Sandrine Georgeon / Stéphane Rosset / Srajan Kapoor / Jagrity Choudhury / Justas Dauparas / ...Authors: Casper A Goverde / Martin Pacesa / Nicolas Goldbach / Lars J Dornfeld / Petra E M Balbi / Sandrine Georgeon / Stéphane Rosset / Srajan Kapoor / Jagrity Choudhury / Justas Dauparas / Christian Schellhaas / Simon Kozlov / David Baker / Sergey Ovchinnikov / Alex J Vecchio / Bruno E Correia /
Abstract: De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of ...De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses demonstrate the high thermal stability of the designs, and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, as a proof of concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we have designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.
#1: Journal: Biorxiv / Year: 2024
Title: Computational design of soluble functional analogues of integral membrane proteins.
Authors: Goverde, C.A. / Pacesa, M. / Goldbach, N. / Dornfeld, L.J. / Balbi, P.E.M. / Georgeon, S. / Rosset, S. / Kapoor, S. / Choudhury, J. / Dauparas, J. / Schellhaas, C. / Kozlov, S. / Baker, D. / ...Authors: Goverde, C.A. / Pacesa, M. / Goldbach, N. / Dornfeld, L.J. / Balbi, P.E.M. / Georgeon, S. / Rosset, S. / Kapoor, S. / Choudhury, J. / Dauparas, J. / Schellhaas, C. / Kozlov, S. / Baker, D. / Ovchinnikov, S. / Vecchio, A.J. / Correia, B.E.
History
DepositionMay 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 14, 2024Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed TIM-barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7173
Polymers19,6461
Non-polymers712
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-20 kcal/mol
Surface area9110 Å2
Unit cell
Length a, b, c (Å)36.629, 44.407, 125.459
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 De novo designed TIM-barrel


Mass: 19645.688 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)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M Na3 Cit, 1 M LiCl, 20% PEG 6k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→62.73 Å / Num. obs: 46891 / % possible obs: 99.87 % / Redundancy: 9.2 % / Biso Wilson estimate: 21.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05821 / Net I/σ(I): 15.64
Reflection shellResolution: 1.34→1.388 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.422 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 4601 / CC1/2: 0.726 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→62.73 Å / SU ML: 0.1395 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1885 2383 5.08 %
Rwork0.1673 44508 -
obs0.1685 46891 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.06 Å2
Refinement stepCycle: LAST / Resolution: 1.34→62.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1367 0 2 232 1601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631405
X-RAY DIFFRACTIONf_angle_d0.8381901
X-RAY DIFFRACTIONf_chiral_restr0.0655237
X-RAY DIFFRACTIONf_plane_restr0.0054239
X-RAY DIFFRACTIONf_dihedral_angle_d12.4838531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.370.35091430.30352562X-RAY DIFFRACTION99.96
1.37-1.40.27241190.26312594X-RAY DIFFRACTION99.96
1.4-1.430.29781370.2262575X-RAY DIFFRACTION100
1.43-1.470.20661220.20492620X-RAY DIFFRACTION99.96
1.47-1.50.22591390.17742562X-RAY DIFFRACTION100
1.5-1.550.21681280.17882601X-RAY DIFFRACTION99.82
1.55-1.60.20771420.17522597X-RAY DIFFRACTION99.31
1.6-1.660.19551360.15312573X-RAY DIFFRACTION99.93
1.66-1.720.18881400.14362596X-RAY DIFFRACTION100
1.72-1.80.17581450.13962595X-RAY DIFFRACTION99.96
1.8-1.90.20411400.14712602X-RAY DIFFRACTION99.96
1.9-2.010.191420.16012627X-RAY DIFFRACTION99.96
2.01-2.170.17241430.14572618X-RAY DIFFRACTION100
2.17-2.390.16491620.14642630X-RAY DIFFRACTION100
2.39-2.730.18961380.15942660X-RAY DIFFRACTION100
2.73-3.440.19521450.1742687X-RAY DIFFRACTION99.54
3.45-62.730.17921620.17422809X-RAY DIFFRACTION99.5

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