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- PDB-8szz: CryoEM Structure of Computationally Designed Nanocage O32-ZL4 -

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Basic information

Entry
Database: PDB / ID: 8szz
TitleCryoEM Structure of Computationally Designed Nanocage O32-ZL4
Components
  • O32-ZL4 Component A
  • O32-ZL4 Component B
KeywordsDE NOVO PROTEIN / O32-ZL4
Function / homologyKDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase-type TIM barrel / lyase activity / 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Function and homology information
Biological speciesThermotoga maritima (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWeidle, C. / Borst, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Mater / Year: 2023
Title: Accurate computational design of three-dimensional protein crystals.
Authors: Zhe Li / Shunzhi Wang / Una Nattermann / Asim K Bera / Andrew J Borst / Muammer Y Yaman / Matthew J Bick / Erin C Yang / William Sheffler / Byeongdu Lee / Soenke Seifert / Greg L Hura / ...Authors: Zhe Li / Shunzhi Wang / Una Nattermann / Asim K Bera / Andrew J Borst / Muammer Y Yaman / Matthew J Bick / Erin C Yang / William Sheffler / Byeongdu Lee / Soenke Seifert / Greg L Hura / Hannah Nguyen / Alex Kang / Radhika Dalal / Joshua M Lubner / Yang Hsia / Hugh Haddox / Alexis Courbet / Quinton Dowling / Marcos Miranda / Andrew Favor / Ali Etemadi / Natasha I Edman / Wei Yang / Connor Weidle / Banumathi Sankaran / Babak Negahdari / Michael B Ross / David S Ginger / David Baker /
Abstract: Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing ...Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.
History
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: O32-ZL4 Component A
1: O32-ZL4 Component A
2: O32-ZL4 Component A
3: O32-ZL4 Component A
I: O32-ZL4 Component B
J: O32-ZL4 Component B
K: O32-ZL4 Component B
L: O32-ZL4 Component B
M: O32-ZL4 Component B
N: O32-ZL4 Component B
O: O32-ZL4 Component B
P: O32-ZL4 Component A
Q: O32-ZL4 Component A
R: O32-ZL4 Component A
S: O32-ZL4 Component A
T: O32-ZL4 Component A
U: O32-ZL4 Component B
V: O32-ZL4 Component A
W: O32-ZL4 Component A
X: O32-ZL4 Component A
Y: O32-ZL4 Component B
Z: O32-ZL4 Component B
a: O32-ZL4 Component B
b: O32-ZL4 Component B
c: O32-ZL4 Component B
d: O32-ZL4 Component B
e: O32-ZL4 Component B
f: O32-ZL4 Component B
g: O32-ZL4 Component B
h: O32-ZL4 Component B
i: O32-ZL4 Component B
j: O32-ZL4 Component B
k: O32-ZL4 Component B
l: O32-ZL4 Component B
m: O32-ZL4 Component B
n: O32-ZL4 Component B
o: O32-ZL4 Component A
p: O32-ZL4 Component A
q: O32-ZL4 Component A
r: O32-ZL4 Component A
s: O32-ZL4 Component A
t: O32-ZL4 Component A
u: O32-ZL4 Component A
v: O32-ZL4 Component A
w: O32-ZL4 Component A
x: O32-ZL4 Component A
y: O32-ZL4 Component A
z: O32-ZL4 Component A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)767,03072
Polymers766,47948
Non-polymers55224
Water00
1


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

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Components

#1: Protein ...
O32-ZL4 Component A


Mass: 8766.459 Da / Num. of mol.: 24 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein ...
O32-ZL4 Component B


Mass: 23170.152 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0066 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WXS1
#3: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Na
Has ligand of interestN
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: O32-ZL4 / Type: COMPLEX
Details: These two proteins were co expressed from the same plasmid and assembled inside E. coli into cages. O32-ZL4 was purified using the His tag on B component
Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.76491792 MDa / Experimental value: YES
Source (natural)Organism: Thermotoga maritima (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.5 / Details: 25 mM Tris/HCl pH 7.5, 150 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris HCl pH 7.5C4H11NO3HCl1
2150 mMSodium ChlorideNaCl1
SpecimenConc.: 2.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 25 mM Tris, 150 mM NaCl
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 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 FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
13Cootmodel refinement
14PHENIXmodel refinement
15Rosettamodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 673044
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 674044 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 144.9 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingDetails: Computational model / Source name: Other / Type: in silico model

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