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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: To Be Published
Title: De novo design of quasi-symmetric two-component protein cages
Authors: Wang, S. / Xie, Y. / Chemielewski, D. / Weidle, C. / Hernandez, C. / Chen, W. / Ahn, G. / Duran, D.C. / Bera, A.K. / Bethel, N. / Decarreau, J. / Tong, S. / Kang, A. / Brackenbrough, E. / ...Authors: Wang, S. / Xie, Y. / Chemielewski, D. / Weidle, C. / Hernandez, C. / Chen, W. / Ahn, G. / Duran, D.C. / Bera, A.K. / Bethel, N. / Decarreau, J. / Tong, S. / Kang, A. / Brackenbrough, E. / Joyce, E. / Lee, S. / Wu, K. / Borst, A.J. / Favor, A. / Buwei, H. / DiMaio, F. / Holt, L. / Baker, D.
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

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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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