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- PDB-9om3: Two Component Protein Nano-Particle (T=3). De Novo Design, Comput... -

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Basic information

Entry
Database: PDB / ID: 9om3
TitleTwo Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Single Particle CryoEM Map with Icosahedral Symmetry Applied
Components
  • C2-B
  • C3-A
KeywordsDE NOVO PROTEIN / Goldberg icosahedron / C60 / Fullerene
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17.45 Å
AuthorsDiMaio, F. / Weidle, C.
Funding support United States, France, 8items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-19-1-0003 United States
Burroughs Wellcome Fund United States
Human Frontier Science Program (HFSP)RGP0061/2019 France
Bill & Melinda Gates FoundationINV-043758 United States
Bill & Melinda Gates FoundationOPP1156262 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG063845 United States
Department of Energy (DOE, United States)KP1607011 United States
CitationJournal: Nature / Year: 2026
Title: De novo design of quasisymmetric two-component protein cages.
Authors: Shunzhi Wang / Ying Xie / David Chmielewski / 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 Chmielewski / 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
DepositionMay 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C2-B
B: C3-A
C: C2-B
D: C3-A
E: C2-B
F: C3-A
G: C2-B
H: C3-A
I: C2-B
J: C3-A
K: C2-B
L: C3-A
M: C2-B
N: C3-A
O: C2-B
P: C3-A
Q: C2-B
R: C3-A
S: C2-B
T: C3-A
U: C2-B
V: C3-A
W: C2-B
X: C3-A
Y: C2-B
Z: C3-A
a: C2-B
b: C3-A
c: C2-B
d: C3-A
e: C2-B
f: C3-A
g: C2-B
h: C3-A
i: C2-B
j: C3-A
k: C2-B
l: C3-A
m: C2-B
n: C3-A
o: C2-B
p: C3-A
q: C2-B
r: C3-A
s: C2-B
t: C3-A
u: C2-B
v: C3-A
w: C2-B
x: C3-A
y: C2-B
z: C3-A
ZA: C2-B
ZB: C3-A
ZC: C2-B
ZD: C3-A
ZE: C2-B
ZF: C3-A
ZG: C2-B
ZH: C3-A
ZI: C2-B
ZJ: C3-A
AA: C2-B
AB: C3-A
AC: C2-B
AD: C3-A
AE: C2-B
AF: C3-A
AG: C2-B
AH: C3-A
AI: C2-B
AJ: C3-A
AK: C2-B
AL: C3-A
AM: C2-B
AN: C3-A
AO: C2-B
AP: C3-A
AQ: C2-B
AR: C3-A
AS: C2-B
AT: C3-A
AU: C2-B
AV: C3-A
AW: C2-B
AX: C3-A
AY: C2-B
AZ: C3-A
Aa: C2-B
Ab: C3-A
Ac: C2-B
Ad: C3-A
Ae: C2-B
Af: C3-A
Ag: C2-B
Ah: C3-A
Ai: C2-B
Aj: C3-A
Ak: C2-B
Al: C3-A
Am: C2-B
An: C3-A
Ao: C2-B
Ap: C3-A
Aq: C2-B
Ar: C3-A
As: C2-B
At: C3-A
Au: C2-B
Av: C3-A
Aw: C2-B
Ax: C3-A
Ay: C2-B
Az: C3-A
ZK: C2-B
ZL: C3-A
ZM: C2-B
ZN: C3-A
ZO: C2-B
ZP: C3-A
ZQ: C2-B
ZR: C3-A
ZS: C2-B
ZT: C3-A
BA: C2-B
BB: C3-A
BC: C2-B
BD: C3-A
BE: C2-B
BF: C3-A
BG: C2-B
BH: C3-A
BI: C2-B
BJ: C3-A
BK: C2-B
BL: C3-A
BM: C2-B
BN: C3-A
BO: C2-B
BP: C3-A
BQ: C2-B
BR: C3-A
BS: C2-B
BT: C3-A
BU: C2-B
BV: C3-A
BW: C2-B
BX: C3-A
BY: C2-B
BZ: C3-A
Ba: C2-B
Bb: C3-A
Bc: C2-B
Bd: C3-A
Be: C2-B
Bf: C3-A
Bg: C2-B
Bh: C3-A
Bi: C2-B
Bj: C3-A
Bk: C2-B
Bl: C3-A
Bm: C2-B
Bn: C3-A
Bo: C2-B
Bp: C3-A
Bq: C2-B
Br: C3-A
Bs: C2-B
Bt: C3-A
Bu: C2-B
Bv: C3-A
Bw: C2-B
Bx: C3-A
By: C2-B
Bz: C3-A
ZU: C2-B
ZV: C3-A
ZW: C2-B
ZX: C3-A
ZY: C2-B
ZZ: C3-A
YA: C2-B
YB: C3-A
YC: C2-B
YD: C3-A
CA: C2-B
CB: C3-A
CC: C2-B
CD: C3-A
CE: C2-B
CF: C3-A
CG: C2-B
CH: C3-A
CI: C2-B
CJ: C3-A
CK: C2-B
CL: C3-A
CM: C2-B
CN: C3-A
CO: C2-B
CP: C3-A
CQ: C2-B
CR: C3-A
CS: C2-B
CT: C3-A
CU: C2-B
CV: C3-A
CW: C2-B
CX: C3-A
CY: C2-B
CZ: C3-A
Ca: C2-B
Cb: C3-A
Cc: C2-B
Cd: C3-A
Ce: C2-B
Cf: C3-A
Cg: C2-B
Ch: C3-A
Ci: C2-B
Cj: C3-A
Ck: C2-B
Cl: C3-A
Cm: C2-B
Cn: C3-A
Co: C2-B
Cp: C3-A
Cq: C2-B
Cr: C3-A
Cs: C2-B
Ct: C3-A
Cu: C2-B
Cv: C3-A
Cw: C2-B
Cx: C3-A
Cy: C2-B
Cz: C3-A
YE: C2-B
YF: C3-A
YG: C2-B
YH: C3-A
YI: C2-B
YJ: C3-A
YK: C2-B
YL: C3-A
YM: C2-B
YN: C3-A
DA: C2-B
DB: C3-A
DC: C2-B
DD: C3-A
DE: C2-B
DF: C3-A
DG: C2-B
DH: C3-A
DI: C2-B
DJ: C3-A
DK: C2-B
DL: C3-A
DM: C2-B
DN: C3-A
DO: C2-B
DP: C3-A
DQ: C2-B
DR: C3-A
DS: C2-B
DT: C3-A
DU: C2-B
DV: C3-A
DW: C2-B
DX: C3-A
DY: C2-B
DZ: C3-A
Da: C2-B
Db: C3-A
Dc: C2-B
Dd: C3-A
De: C2-B
Df: C3-A
Dg: C2-B
Dh: C3-A
Di: C2-B
Dj: C3-A
Dk: C2-B
Dl: C3-A
Dm: C2-B
Dn: C3-A
Do: C2-B
Dp: C3-A
Dq: C2-B
Dr: C3-A
Ds: C2-B
Dt: C3-A
Du: C2-B
Dv: C3-A
Dw: C2-B
Dx: C3-A
Dy: C2-B
Dz: C3-A
YO: C2-B
YP: C3-A
YQ: C2-B
YR: C3-A
YS: C2-B
YT: C3-A
YU: C2-B
YV: C3-A
YW: C2-B
YX: C3-A
EA: C2-B
EB: C3-A
EC: C2-B
ED: C3-A
EE: C2-B
EF: C3-A
EG: C2-B
EH: C3-A
EI: C2-B
EJ: C3-A
EK: C2-B
EL: C3-A
EM: C2-B
EN: C3-A
EO: C2-B
EP: C3-A
EQ: C2-B
ER: C3-A
ES: C2-B
ET: C3-A
EU: C2-B
EV: C3-A
EW: C2-B
EX: C3-A
EY: C2-B
EZ: C3-A
Ea: C2-B
Eb: C3-A
Ec: C2-B
Ed: C3-A
Ee: C2-B
Ef: C3-A
Eg: C2-B
Eh: C3-A
Ei: C2-B
Ej: C3-A
Ek: C2-B
El: C3-A
Em: C2-B
En: C3-A
Eo: C2-B
Ep: C3-A
Eq: C2-B
Er: C3-A
Es: C2-B
Et: C3-A
Eu: C2-B
Ev: C3-A
Ew: C2-B
Ex: C3-A


Theoretical massNumber of molelcules
Total (without water)8,275,129360
Polymers8,275,129360
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
C2-B


Mass: 12591.434 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21* (DE3)
#2: Protein ...
C3-A


Mass: 33381.504 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21* (DE3)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Protein structure is equivalent to a C60 fullerene and has the general shape of a soccer ball with 12 pentagonal and 20 hexagonal facets. There are a total of 60 vertices (C3-A) and 90 edges (C2-B)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain: BL21* (DE3)
Buffer solutionpH: 8.5 / Details: 25 mM Tris-HCl and 300 mM NaCl (pH 8)
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMtris(hydroxymethyl)aminomethane Hydrochloric AcidTris-HCl1
2300 mMSodium ChlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 48.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7290
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7Rosettamodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 142674
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 17.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11155 / Algorithm: FOURIER SPACE / Details: Homogeneous Refinement / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: Computational Design / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 16.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0171557880
ELECTRON MICROSCOPYf_angle_d1.4345752340
ELECTRON MICROSCOPYf_chiral_restr0.086491620
ELECTRON MICROSCOPYf_plane_restr0.007397080
ELECTRON MICROSCOPYf_dihedral_angle_d9.1254215700

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