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- PDB-8v3b: Computational Designed Nanocage O43_129_+4 -

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Basic information

Entry
Database: PDB / ID: 8v3b
TitleComputational Designed Nanocage O43_129_+4
Components
  • O43_129_+4 component A
  • O43_129_+4 component B
KeywordsDE NOVO PROTEIN / O43 / Nanocage / De Novo / Programmable Design
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsCarr, K.D. / Weidle, C. / Borst, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2024
Title: Blueprinting extendable nanomaterials with standardized protein blocks.
Authors: Timothy F Huddy / Yang Hsia / Ryan D Kibler / Jinwei Xu / Neville Bethel / Deepesh Nagarajan / Rachel Redler / Philip J Y Leung / Connor Weidle / Alexis Courbet / Erin C Yang / Asim K Bera / ...Authors: Timothy F Huddy / Yang Hsia / Ryan D Kibler / Jinwei Xu / Neville Bethel / Deepesh Nagarajan / Rachel Redler / Philip J Y Leung / Connor Weidle / Alexis Courbet / Erin C Yang / Asim K Bera / Nicolas Coudray / S John Calise / Fatima A Davila-Hernandez / Hannah L Han / Kenneth D Carr / Zhe Li / Ryan McHugh / Gabriella Reggiano / Alex Kang / Banumathi Sankaran / Miles S Dickinson / Brian Coventry / T J Brunette / Yulai Liu / Justas Dauparas / Andrew J Borst / Damian Ekiert / Justin M Kollman / Gira Bhabha / David Baker /
Abstract: A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The ...A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight 'train track' assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to 'back of an envelope' architectural blueprints.
History
DepositionNov 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O43_129_+4 component A
B: O43_129_+4 component A
C: O43_129_+4 component A
D: O43_129_+4 component A
E: O43_129_+4 component A
F: O43_129_+4 component A
G: O43_129_+4 component A
H: O43_129_+4 component A
I: O43_129_+4 component A
J: O43_129_+4 component A
K: O43_129_+4 component A
L: O43_129_+4 component A
M: O43_129_+4 component A
N: O43_129_+4 component A
O: O43_129_+4 component A
P: O43_129_+4 component A
Q: O43_129_+4 component A
R: O43_129_+4 component A
S: O43_129_+4 component A
T: O43_129_+4 component A
U: O43_129_+4 component A
V: O43_129_+4 component A
W: O43_129_+4 component A
X: O43_129_+4 component A
a: O43_129_+4 component B
b: O43_129_+4 component B
c: O43_129_+4 component B
d: O43_129_+4 component B
e: O43_129_+4 component B
f: O43_129_+4 component B
g: O43_129_+4 component B
h: O43_129_+4 component B
i: O43_129_+4 component B
j: O43_129_+4 component B
k: O43_129_+4 component B
l: O43_129_+4 component B
m: O43_129_+4 component B
n: O43_129_+4 component B
o: O43_129_+4 component B
p: O43_129_+4 component B
q: O43_129_+4 component B
r: O43_129_+4 component B
s: O43_129_+4 component B
t: O43_129_+4 component B
u: O43_129_+4 component B
v: O43_129_+4 component B
w: O43_129_+4 component B
x: O43_129_+4 component B


Theoretical massNumber of molelcules
Total (without water)1,935,66948
Polymers1,935,66948
Non-polymers00
Water0
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 ...
O43_129_+4 component A


Mass: 33976.965 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein ...
O43_129_+4 component B


Mass: 46675.922 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: Computational Designed Nanocage O43_129_+4 / Type: COMPLEX
Details: Chain A and chain B were expressed separately in E. coli. Complex was formed by mixing the lysis of chain A and chain B. Sample was purified through HIS-tag on chain A.
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: unidentified (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 300mM NaCl, 25mM Tris-HCL
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMSodium ChlorideNaClSodium chloride1
225 mMTRIStrisHCl1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.0particle selection
2SerialEMimage acquisition
4cryoSPARC4.4.0CTF correction
7UCSF ChimeraX1.6.1model fitting
9cryoSPARC4.4.0initial Euler assignment
10cryoSPARC4.4.0final Euler assignment
11cryoSPARC4.4.0classification
12cryoSPARC4.4.03D reconstruction
13PHENIXdev-4761model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 23522
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16878 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 804.6 / Protocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Computationally designed model was docked into experimentally derived volume map in ChimeraX. It was then relaxed using Namdinator. Then it was trimmed to polyA in PHENIX.

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