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- PDB-8flx: De novo designed homotrimer; the fusion product of BGL17 and DHR59 -

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Basic information

Entry
Database: PDB / ID: 8flx
TitleDe novo designed homotrimer; the fusion product of BGL17 and DHR59
ComponentsLK031
KeywordsDE NOVO PROTEIN / de novo / computationally designed / designed / tandem repeat protein / kibloid / homotrimer
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsKibler, R.D. / Kennedy, M.A. / Stoddard, B.L. / Lee, S.
Funding support United States, 6items
OrganizationGrant numberCountry
Other privateMacCoss Yeast P41
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5P41GM103533 United States
National Science Foundation (NSF, United States)DGE-1762114 United States
Other privateAudacious Project philanthropic funds
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM105691 United States
Other government1S10D028581-01
CitationJournal: Nature / Year: 2025
Title: Four-component protein nanocages designed by programmed symmetry breaking.
Authors: Sangmin Lee / Ryan D Kibler / Green Ahn / Yang Hsia / Andrew J Borst / Annika Philomin / Madison A Kennedy / Buwei Huang / Barry Stoddard / David Baker /
Abstract: Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral or icosahedral point group symmetry to generate closed cage-like structures. Viruses access more ...Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral or icosahedral point group symmetry to generate closed cage-like structures. Viruses access more complex higher triangulation number icosahedral architectures by breaking perfect point group symmetry, but nature appears not to have explored similar symmetry breaking for tetrahedral or octahedral symmetries. Here we describe a general design strategy for building higher triangulation number architectures starting from regular polyhedra through pseudosymmetrization of trimeric building blocks. Electron microscopy confirms the structures of T = 4 cages with 48 (tetrahedral), 96 (octahedral) and 240 (icosahedral) subunits, each with 4 distinct chains and 6 different protein-protein interfaces, and diameters of 33 nm, 43 nm and 75 nm, respectively. Higher triangulation number viruses possess very sophisticated functionalities; our general route to higher triangulation number nanocages should similarly enable a next generation of multiple antigen-displaying vaccine candidates and targeted delivery vehicles.
History
DepositionDec 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Dec 25, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LK031


Theoretical massNumber of molelcules
Total (without water)38,6781
Polymers38,6781
Non-polymers00
Water00
1
A: LK031

A: LK031

A: LK031


Theoretical massNumber of molelcules
Total (without water)116,0343
Polymers116,0343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area2170 Å2
ΔGint-27 kcal/mol
Surface area50000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.477, 153.477, 153.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein LK031


Mass: 38677.871 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)
Has protein modificationN

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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: 3.89 Å3/Da / Density % sol: 68.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Ammonium citrate tribasic pH 7.0, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 6944 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 1.003 / Χ2: 0.028 / Net I/σ(I): 4.4 / Num. measured all: 69242
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
4.5-4.6670.7966900.421100
4.66-4.859.70.6827040.4151100
4.85-5.0710.50.6896910.4221100
5.07-5.3310.50.5646880.4141100
5.33-5.679.90.5357120.4161100
5.67-6.1110.40.3446730.4271100
6.11-6.7210.50.1967040.431100
6.72-7.6910.60.0786820.4661100
7.69-9.6710.10.0416970.571100
9.67-5010.50.0387030.6061100

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
HKL-2000data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.5→48.53 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 49.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3441 361 10 %
Rwork0.302 --
obs0.3064 3609 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.5→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 0 0 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d6.603342
X-RAY DIFFRACTIONf_chiral_restr0.032338
X-RAY DIFFRACTIONf_plane_restr0.002347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5-5.150.48561120.41261056X-RAY DIFFRACTION96
5.16-6.490.43051180.46351055X-RAY DIFFRACTION97
6.5-48.530.3021310.24061137X-RAY DIFFRACTION100

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