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- PDB-8ed3: Structure of a nanoparticle with icosahedral symmetry -

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Basic information

Entry
Database: PDB / ID: 8ed3
TitleStructure of a nanoparticle with icosahedral symmetry
ComponentsDesigned I3-01 icosahedron
KeywordsDE NOVO PROTEIN / Protein design / nanoparticle
Function / homology4-hydroxy-2-oxoglutarate aldolase / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase-type TIM barrel / 4-Hydroxy-2-oxoglutarate aldolase / 2-dehydro-3-deoxyphosphogluconate aldolase
Function and homology information
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMcCarthy, S. / Gonen, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Heliyon / Year: 2022
Title: Improved interface packing and design opportunities revealed by CryoEM analysis of a designed protein nanocage.
Authors: Stephen McCarthy / Shane Gonen /
Abstract: Symmetric protein assemblies play important roles in nature which makes them an attractive target for engineering. symmetric protein complexes can be created through computational protein design to ...Symmetric protein assemblies play important roles in nature which makes them an attractive target for engineering. symmetric protein complexes can be created through computational protein design to tailor their properties from first principles, and recently several protein nanocages have been created by bringing together protein components through hydrophobic interactions. Accurate experimental structures of newly-developed proteins are essential to validate their design, improve assembly stability, and tailor downstream applications. We describe the CryoEM structure of the nanocage I3-01, at an overall resolution of 3.5 Å. I3-01, comprising 60 aldolase subunits arranged with icosahedral symmetry, has resisted high-resolution characterization. Some key differences between the refined structure and the original design are identified, such as improved packing of hydrophobic sidechains, providing insight to the resistance of I3-01 to high-resolution averaging. Based on our analysis, we suggest factors important in the design and structural processing of new assemblies.
History
DepositionSep 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed I3-01 icosahedron
B: Designed I3-01 icosahedron
C: Designed I3-01 icosahedron
D: Designed I3-01 icosahedron
E: Designed I3-01 icosahedron
F: Designed I3-01 icosahedron
G: Designed I3-01 icosahedron
H: Designed I3-01 icosahedron
I: Designed I3-01 icosahedron
J: Designed I3-01 icosahedron
K: Designed I3-01 icosahedron
L: Designed I3-01 icosahedron
M: Designed I3-01 icosahedron
N: Designed I3-01 icosahedron
O: Designed I3-01 icosahedron
P: Designed I3-01 icosahedron
Q: Designed I3-01 icosahedron
R: Designed I3-01 icosahedron
S: Designed I3-01 icosahedron
T: Designed I3-01 icosahedron
U: Designed I3-01 icosahedron
V: Designed I3-01 icosahedron
W: Designed I3-01 icosahedron
X: Designed I3-01 icosahedron
Y: Designed I3-01 icosahedron
Z: Designed I3-01 icosahedron
0: Designed I3-01 icosahedron
1: Designed I3-01 icosahedron
2: Designed I3-01 icosahedron
3: Designed I3-01 icosahedron
4: Designed I3-01 icosahedron
5: Designed I3-01 icosahedron
6: Designed I3-01 icosahedron
7: Designed I3-01 icosahedron
8: Designed I3-01 icosahedron
9: Designed I3-01 icosahedron
a: Designed I3-01 icosahedron
b: Designed I3-01 icosahedron
c: Designed I3-01 icosahedron
d: Designed I3-01 icosahedron
e: Designed I3-01 icosahedron
f: Designed I3-01 icosahedron
g: Designed I3-01 icosahedron
h: Designed I3-01 icosahedron
i: Designed I3-01 icosahedron
j: Designed I3-01 icosahedron
k: Designed I3-01 icosahedron
l: Designed I3-01 icosahedron
m: Designed I3-01 icosahedron
n: Designed I3-01 icosahedron
o: Designed I3-01 icosahedron
p: Designed I3-01 icosahedron
q: Designed I3-01 icosahedron
r: Designed I3-01 icosahedron
s: Designed I3-01 icosahedron
t: Designed I3-01 icosahedron
u: Designed I3-01 icosahedron
v: Designed I3-01 icosahedron
w: Designed I3-01 icosahedron
x: Designed I3-01 icosahedron


Theoretical massNumber of molelcules
Total (without water)1,299,63560
Polymers1,299,63560
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Designed I3-01 icosahedron / 4-Hydroxy-2-oxoglutarate aldolase / 2-dehydro-3-deoxyphosphogluconate aldolase


Mass: 21660.584 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: Tmari_0063 / Production host: Escherichia coli (E. coli)
References: UniProt: G4FGY1, 2-dehydro-3-deoxy-phosphogluconate aldolase, 4-hydroxy-2-oxoglutarate aldolase
Has protein modificationY

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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: I3-01 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 2.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
7UCSF Chimeramodel fitting
9Rosettamodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147349 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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