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- PDB-8oyx: De novo designed soluble GPCR-like fold GLF_18 -

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Basic information

Entry
Database: PDB / ID: 8oyx
TitleDe novo designed soluble GPCR-like fold GLF_18
ComponentsDe novo designed soluble GPCR-like protein
KeywordsDE NOVO PROTEIN / GPCR / solubilized / de novo designed
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 1.1Nov 15, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 14, 2024Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: De novo designed soluble GPCR-like protein
B: De novo designed soluble GPCR-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6564
Polymers55,4662
Non-polymers1902
Water79344
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A: De novo designed soluble GPCR-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8282
Polymers27,7331
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo designed soluble GPCR-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8282
Polymers27,7331
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.726, 52.084, 58.392
Angle α, β, γ (deg.)94.080, 104.360, 110.800
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 2 or resid 4...
d_2ens_1(chain "B" and (resid 1 through 2 or resid 4...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYARGA1 - 2
d_12ens_1GLUGLUA4 - 18
d_13ens_1ALAGLUA20 - 65
d_14ens_1VALARGA67 - 98
d_15ens_1PROILEA106 - 112
d_16ens_1ALAALAA114 - 176
d_17ens_1ASNILEA178 - 194
d_18ens_1GLUALAA196 - 232
d_19ens_1PO4PO4B
d_21ens_1GLYARGC1 - 2
d_22ens_1GLUGLUC4 - 18
d_23ens_1ALAGLUC20 - 65
d_24ens_1VALILEC67 - 105
d_25ens_1ALAALAC107 - 169
d_26ens_1ASNILEC171 - 187
d_27ens_1GLUALAC189 - 225
d_28ens_1PO4PO4D

NCS oper: (Code: givenMatrix: (0.999052582918, -0.0068313051023, -0.0429798770902), (-0.00657714193963, -0.999960055414, 0.00605217146371), (-0.0430195045067, -0.00576375278091, -0.99905760664)Vector: ...NCS oper: (Code: given
Matrix: (0.999052582918, -0.0068313051023, -0.0429798770902), (-0.00657714193963, -0.999960055414, 0.00605217146371), (-0.0430195045067, -0.00576375278091, -0.99905760664)
Vector: -0.60424512891, -38.8545768267, -23.548558342)

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Components

#1: Protein De novo designed soluble GPCR-like protein


Mass: 27732.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: Na Phos Cit pH 4.2, 0.2 M LiSO4, 20% PEG 1000

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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: Feb 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→47.93 Å / Num. obs: 20309 / % possible obs: 88.48 % / Redundancy: 1.7 % / Biso Wilson estimate: 36.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04953 / Net I/σ(I): 9.89
Reflection shellResolution: 2.11→2.185 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.35 / Num. unique obs: 2144 / CC1/2: 0.748 / % possible all: 92.81

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→47.93 Å / SU ML: 0.2782 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.55
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2507 1017 5.01 %
Rwork0.2025 19292 -
obs0.2049 20309 88.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.5 Å2
Refinement stepCycle: LAST / Resolution: 2.11→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 10 44 3740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573739
X-RAY DIFFRACTIONf_angle_d0.87715045
X-RAY DIFFRACTIONf_chiral_restr0.0501588
X-RAY DIFFRACTIONf_plane_restr0.0078651
X-RAY DIFFRACTIONf_dihedral_angle_d5.663488
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.668379666205 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.220.32241470.25052864X-RAY DIFFRACTION91.97
2.22-2.350.26871520.23112816X-RAY DIFFRACTION90.08
2.35-2.540.26811720.22622723X-RAY DIFFRACTION88.97
2.54-2.790.30091350.21612751X-RAY DIFFRACTION87.99
2.79-3.20.26451190.22132670X-RAY DIFFRACTION84.9
3.2-4.030.25961550.18922658X-RAY DIFFRACTION85.79
4.03-47.930.20961370.18312810X-RAY DIFFRACTION89.82
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)
12.230767277880.6803222707021.03796582485.598677797343.006023837692.770540263050.0554965312235-0.75327324723-0.04402038953260.0464577136411-0.5933600897920.5888114853630.255077922464-1.557040643050.009501255187090.353211118481-0.09413727295980.04666775307650.5958425634960.03630201901920.4329789222-20.8391992734-7.7614045036-1.35216008227
21.759169759251.02866526349-2.412474207581.11877446486-2.225639921554.627650808690.9183332003970.715344789203-0.579740974715-1.879140803791.2777194472-0.1072455735831.33676943353-0.694339554798-0.06804580050921.02561004547-0.2962499454890.1211371004360.65285551844-0.08646349761340.783134141706-18.5194714064-16.6730761562-22.9823669968
33.974011729680.6921554518570.9789715186253.214731461620.4011924250498.07953751260.121420943257-0.449878973688-0.5871351190310.225585016142-0.0928337553743-0.08882957278831.695680138680.0980823796585-0.07510707993340.31762709697-0.0221383387739-0.1063780046640.2716940149110.09906617371750.448582568112-11.9239290756-11.7352801072-1.88122788079
42.489236500070.7146062139660.1063953719922.98438814580.4748470062552.619999014680.0801869606770.0248234053149-0.338653395064-0.2282639375110.1536835883810.01237467392990.7125337150240.199366450389-0.1656594535720.2517895328580.0492909902906-0.02044951607220.227844915071-0.03411093057090.402643708086-3.87523132338-9.47047976483-10.4441477132
53.31377507269-0.03879924452310.4384536284162.91314203207-0.04122609023826.639123713440.0489211930880.06521653687730.0958204870188-0.419498604626-0.224705217050.1495771846550.7178048452150.912353529243-0.04991174430560.3670139918820.0168088868509-0.03240106874370.315404996658-0.09946535048640.5636330065962.67724080644-14.104170396-12.8418474066
63.146447282620.124328961151-0.7550498568662.35079578472-0.6582044435085.335417197230.153151656978-0.1702159729590.149973679904-0.0796233225595-0.0429351326169-0.219761006254-0.3484869172570.282010673179-0.1662485357220.219804637981-0.04053551662590.02961054555280.18617017791-0.01224005983730.287188432192-1.408561647911.26921001678-6.6526037531
73.30371082572-0.2669133571412.221270006751.75994196519-0.0995732307967.080410429660.00832082033546-0.6297153799230.08557022958630.2099288248490.2325802650240.0571062364301-0.55086906908-0.484535596971-0.07511522057240.2512476040160.01423224019790.03273940052950.28320210853-0.000781631853410.206921708836-10.8906692166-0.1038913183972.38911964133
83.048556969270.3582414992613.778918921136.522908838940.01804657861074.70260451939-0.422894860750.25003886006-0.640868711026-1.466618553570.3732529273630.3773235693730.416638863026-0.710332184117-0.2715655676460.516213680772-0.105868091925-0.03969144824910.265132077418-0.04110103661970.335191114242-19.6779319846-5.31284776302-18.5759686228
93.55843031439-0.259019406766-0.7290048177056.09286996083.240558030313.304033136060.05083258487030.4871141996550.157678580029-0.276598126184-0.5706421926380.720254158706-0.449440351442-2.249721152650.6488944952940.388905870990.0581776448536-0.08147851101810.5574206928390.02908209713720.464693202015-21.2803540449-30.876894754-21.426738314
102.45024983642-0.2578489852521.299016603832.691065978560.4047400062184.60344057953-0.17602909163-0.03415631941180.2661901509440.400501748892-0.08059943551980.153659791151-0.471997095148-0.2375396604740.3812043706840.32993804097-0.002258820174730.0382409955770.1842990077320.005113903852420.351060815888-9.09642344238-27.372750877-16.2520933689
112.632541798640.755257727763-0.3980550526242.985130767750.05183522682524.375098918440.1251540856750.02768620842710.2294667206990.1354254788160.0604621931845-0.181719245495-0.1957696421590.598166250836-0.1188487375560.2382808491980.0326776657429-0.009593220015010.289763664052-0.02148938857460.3986528601542.7220074443-30.8392459712-15.2646867383
123.45904315106-0.3959941811150.4339059822692.93079469752-0.7140385938763.18960938333-0.0323674072642-0.167129735825-0.455722797250.1757211131170.03136321574110.1460905441470.3772374493430.06280535884070.01470072937810.24839200904-0.0145904797819-0.01081948096670.2222561091820.01658258503170.258851121967-10.0767179529-40.1795047644-16.75249965
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 26 )AA1 - 261 - 26
22chain 'A' and (resid 27 through 35 )AA27 - 3527 - 35
33chain 'A' and (resid 36 through 63 )AA36 - 6336 - 63
44chain 'A' and (resid 64 through 101 )AA64 - 10164 - 101
55chain 'A' and (resid 102 through 136 )AA102 - 136102 - 136
66chain 'A' and (resid 137 through 199 )AA137 - 199137 - 199
77chain 'A' and (resid 200 through 221 )AA200 - 221200 - 221
88chain 'A' and (resid 222 through 232 )AA222 - 232222 - 232
99chain 'B' and (resid 1 through 26 )BC1 - 261 - 26
1010chain 'B' and (resid 27 through 97 )BC27 - 9727 - 97
1111chain 'B' and (resid 98 through 169 )BC98 - 16998 - 162
1212chain 'B' and (resid 170 through 232 )BC170 - 232163 - 225

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