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- PDB-8cwy: Accurate computational design of genetically encoded 3D protein c... -

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Basic information

Entry
Database: PDB / ID: 8cwy
TitleAccurate computational design of genetically encoded 3D protein crystals
Components
  • T32-15-1
  • T32-15-2
KeywordsDE NOVO PROTEIN / 3D crystals / nanocage / de novo design / rosetta / cryoEM
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsLi, Z. / Borst, A.J. / Baker, D.
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 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T32-15-1
B: T32-15-2
C: T32-15-1
D: T32-15-2
E: T32-15-1
F: T32-15-2
G: T32-15-1
H: T32-15-2
I: T32-15-1
J: T32-15-2
K: T32-15-1
L: T32-15-2
M: T32-15-1
N: T32-15-2
O: T32-15-1
P: T32-15-2
Q: T32-15-1
R: T32-15-2
S: T32-15-1
T: T32-15-2
U: T32-15-1
V: T32-15-2
W: T32-15-1
X: T32-15-2


Theoretical massNumber of molelcules
Total (without water)703,09924
Polymers703,09924
Non-polymers00
Water0
1


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

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Components

#1: Protein
T32-15-1


Mass: 49525.008 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein
T32-15-2


Mass: 9066.595 Da / Num. of mol.: 12
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: T32-15 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 5.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
10cryoSPARC3.2initial Euler assignment
11cryoSPARC3.2final Euler assignment
CTF correctionType: NONE
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 511464 / Symmetry type: POINT

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