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- PDB-9ndl: Crystal Structure of C2-B-alpha20 -

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Basic information

Entry
Database: PDB / ID: 9ndl
TitleCrystal Structure of C2-B-alpha20
ComponentsC2-F8
KeywordsDE NOVO PROTEIN / design model / ML/AI / quasi symmetry / nanoparticles
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBera, A.K. / Wang, S. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2026
Title: De novo design of quasisymmetric two-component protein cages.
Authors: Shunzhi Wang / Ying Xie / David Chemielewski / Connor Weidle / Tong Shu / Green Ahn / Ryan D Kibler / Cindy Hernandez / Wei Chen / David Camilo Duran / Ann Carr / Asim K Bera / Sangmin Lee / ...Authors: Shunzhi Wang / Ying Xie / David Chemielewski / Connor Weidle / Tong Shu / Green Ahn / Ryan D Kibler / Cindy Hernandez / Wei Chen / David Camilo Duran / Ann Carr / Asim K Bera / Sangmin Lee / Justin Decarreau / Alex Kang / Evans Brackenbrough / Emily Joyce / Kejia Wu / Andrew J Borst / Andrew Favor / Buwei Huang / Frank DiMaio / Liam J Holt / David Baker /
Abstract: Quasisymmetric icosahedral viral capsids achieve larger sizes than possible with strictly symmetric icosahedra by tessellating pentagons and hexagons using a single subunit that adopts different ...Quasisymmetric icosahedral viral capsids achieve larger sizes than possible with strictly symmetric icosahedra by tessellating pentagons and hexagons using a single subunit that adopts different conformations in symmetrically non-equivalent locations. Recapitulating such quasisymmetric architectures through computational design is a considerable challenge in nanomaterials engineering. Here we introduce a computational design strategy based on geometric frustration to generate two-component, quasisymmetric protein cages with customizable properties. We designed complementary trimeric and dimeric protein components that co-assemble into positively curved local hexagonal assemblies. Hexagonal lattices cannot tile spherical surfaces; instead, the components form closed sphere-like cage assemblies through incorporation of curvature-inducing pentagonal defects, as evidenced by electron microscopy. By designing dimers that encode different local curvatures, we programmed cage dimensions ranging from 40 to over 200 nm in diameter and with molecular weights from 2 MDa to over 50 MDa, comparable with natural virus capsids. We further functionalized these large cages with additional protein domains to enable ribonucleoprotein cargo loading and cellular uptake. Fluorescently labelled cage assemblies expressed in mammalian cells function as rheological probes and cargo recruiters, enabling a systematic study of size-dependent cytoplasmic diffusion and protein localization. Thus, the quasi-symmetry that has long fascinated structural biologists can now be achieved by computational protein design, with immediate applications to biologics delivery and molecular cell biology.
History
DepositionFeb 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Database references / Category: citation / citation_author
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.year
Revision 1.2Jun 3, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C2-F8
B: C2-F8
C: C2-F8


Theoretical massNumber of molelcules
Total (without water)34,5613
Polymers34,5613
Non-polymers00
Water64936
1
A: C2-F8


Theoretical massNumber of molelcules
Total (without water)11,5201
Polymers11,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C2-F8


Theoretical massNumber of molelcules
Total (without water)11,5201
Polymers11,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: C2-F8


Theoretical massNumber of molelcules
Total (without water)11,5201
Polymers11,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.185, 93.301, 60.693
Angle α, β, γ (deg.)90.000, 119.937, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein C2-F8


Mass: 11520.281 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)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.0 M Ammonium sulfate, 0.1 M Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 18, 2024
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.15→28.99 Å / Num. obs: 15664 / % possible obs: 98 % / Redundancy: 4.3 % / Biso Wilson estimate: 35.96 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.7
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1104 / CC1/2: 0.863 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→28.99 Å / SU ML: 0.2518 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2523 1555 10.02 %
Rwork0.2029 13964 -
obs0.2081 15519 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.76 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 0 36 2463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292451
X-RAY DIFFRACTIONf_angle_d0.50923324
X-RAY DIFFRACTIONf_chiral_restr0.0471408
X-RAY DIFFRACTIONf_plane_restr0.0069438
X-RAY DIFFRACTIONf_dihedral_angle_d21.2031951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.220.33191400.25831248X-RAY DIFFRACTION95
2.22-2.30.29951370.25211244X-RAY DIFFRACTION96.78
2.3-2.40.30421450.22851275X-RAY DIFFRACTION97.39
2.4-2.50.2881310.22771277X-RAY DIFFRACTION97.3
2.5-2.640.2761450.22831261X-RAY DIFFRACTION97.3
2.64-2.80.2981460.23391270X-RAY DIFFRACTION96.99
2.8-3.020.29031440.2121271X-RAY DIFFRACTION97.18
3.02-3.320.23721410.20581260X-RAY DIFFRACTION97.22
3.32-3.80.26581360.1961275X-RAY DIFFRACTION96.25
3.8-4.780.2251430.17691266X-RAY DIFFRACTION96.91
4.78-28.990.2121470.18741317X-RAY DIFFRACTION97.99
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)
15.290921488691.01128903855-1.532964350365.768688131651.007518630226.74204676526-0.08696708565510.154472042845-0.117686150707-0.142301020872-0.0234333851342-0.258893873145-0.02219315340410.2405661691690.1008558887850.192699220825-0.0234170111615-0.01379516922140.232196166649-0.02961440575090.22685744802417.6578111866-6.700836541562.9608526064
23.429089575170.995108119358-1.403605626394.52767729334-0.536798141436.023854037440.0510866907107-0.387954432708-0.2418829784350.330271763316-0.105707391657-0.197587493949-0.1392266139050.3075117557260.02835845755210.240909032583-0.00788930342429-0.05867954784540.1716876528330.03717442246210.2704717249980.420839994272-25.118499074113.0703192299
34.05539579066-0.483899230921-1.588523749893.288766762121.468427923776.06606957865-0.07004936051780.149148783460.08942237853690.0212200722675-0.2021310713050.354147325146-0.229780315757-0.9113938046760.2194577307240.2381187261490.0191619035141-0.07470505296630.454428166126-0.1200713655140.3511345548370.2846948898794.358441426119.2426062371
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 106 / Label seq-ID: 1 - 106

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain A and resseq 1:106)AA
22(chain B and resseq 1:106)BB
33(chain C and resseq 1:106)CC

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