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- PDB-9cm1: Novel designed icosahedral nanoparticle I3-D12 -

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Basic information

Entry
Database: PDB / ID: 9cm1
TitleNovel designed icosahedral nanoparticle I3-D12
ComponentsPhosphosulfolactate synthase
KeywordsVIRUS LIKE PARTICLE / Thermophile / nanoparticle / icosahedron / dehydratase
Function / homology
Function and homology information


phosphosulfolactate synthase / phosphosulfolactate synthase activity / coenzyme M biosynthetic process / sulfopyruvate decarboxylase activity
Similarity search - Function
Phosphosulpholactate synthase / (2R)-phospho-3-sulpholactate synthase, ComA / (2R)-phospho-3-sulpholactate synthase, ComA superfamily / (2R)-phospho-3-sulfolactate synthase (ComA) / Aldolase-type TIM barrel
Similarity search - Domain/homology
Phosphosulfolactate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHaas, C.M. / Jasti, N. / Dosey, A.M. / Gillespie, R. / McGowan, J. / Allen, J.D. / Leaf, E.M. / Crispin, M. / DeForest, C. / Kanekiyo, M. / King, N.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Computational design of protein nanoparticle vaccine scaffolds from sequence alone
Authors: Haas, C.M. / Jasti, N. / Dosey, A.M. / Gillespie, R. / Allen, J.D. / Leaf, E.M. / Crispin, M. / DeForest, C. / Kanekiyo, M. / King, N.P.
History
DepositionJul 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data 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
0: Phosphosulfolactate synthase
1: Phosphosulfolactate synthase
2: Phosphosulfolactate synthase
3: Phosphosulfolactate synthase
4: Phosphosulfolactate synthase
5: Phosphosulfolactate synthase
6: Phosphosulfolactate synthase
7: Phosphosulfolactate synthase
8: Phosphosulfolactate synthase
9: Phosphosulfolactate synthase
A: Phosphosulfolactate synthase
B: Phosphosulfolactate synthase
C: Phosphosulfolactate synthase
D: Phosphosulfolactate synthase
E: Phosphosulfolactate synthase
F: Phosphosulfolactate synthase
G: Phosphosulfolactate synthase
H: Phosphosulfolactate synthase
I: Phosphosulfolactate synthase
J: Phosphosulfolactate synthase
K: Phosphosulfolactate synthase
L: Phosphosulfolactate synthase
M: Phosphosulfolactate synthase
N: Phosphosulfolactate synthase
O: Phosphosulfolactate synthase
P: Phosphosulfolactate synthase
Q: Phosphosulfolactate synthase
R: Phosphosulfolactate synthase
S: Phosphosulfolactate synthase
T: Phosphosulfolactate synthase
U: Phosphosulfolactate synthase
V: Phosphosulfolactate synthase
W: Phosphosulfolactate synthase
X: Phosphosulfolactate synthase
Y: Phosphosulfolactate synthase
Z: Phosphosulfolactate synthase
c: Phosphosulfolactate synthase
d: Phosphosulfolactate synthase
e: Phosphosulfolactate synthase
f: Phosphosulfolactate synthase
g: Phosphosulfolactate synthase
h: Phosphosulfolactate synthase
i: Phosphosulfolactate synthase
j: Phosphosulfolactate synthase
k: Phosphosulfolactate synthase
l: Phosphosulfolactate synthase
m: Phosphosulfolactate synthase
n: Phosphosulfolactate synthase
o: Phosphosulfolactate synthase
p: Phosphosulfolactate synthase
q: Phosphosulfolactate synthase
r: Phosphosulfolactate synthase
s: Phosphosulfolactate synthase
t: Phosphosulfolactate synthase
u: Phosphosulfolactate synthase
v: Phosphosulfolactate synthase
w: Phosphosulfolactate synthase
x: Phosphosulfolactate synthase
y: Phosphosulfolactate synthase
z: Phosphosulfolactate synthase


Theoretical massNumber of molelcules
Total (without water)1,753,70160
Polymers1,753,70160
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Phosphosulfolactate synthase


Mass: 29228.348 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: comA / Production host: Escherichia coli (E. coli) / References: UniProt: Q57703
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: Novel designed icosahedral nanoparticle I3-D12 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165931 / Symmetry type: POINT

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