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- EMDB-27031: Accurate computational design of genetically encoded 3D protein c... -

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Basic information

Entry
Database: EMDB / ID: EMD-27031
TitleAccurate computational design of genetically encoded 3D protein crystals
Map dataSharpened
Sample
  • Complex: T32-15
    • Protein or peptide: T32-15-1
    • Protein or peptide: T32-15-2
Keywords3D crystals / nanocage / de novo design / rosetta / cryoEM / DE NOVO PROTEIN
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsLi Z / Borst AJ / Baker D
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27031.png

Downloads & links

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Map

FileDownload / File: emd_27031.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened
Voxel sizeX=Y=Z: 1.0288 Å
Density
Contour LevelBy AUTHOR: 0.121
Minimum - Maximum-1.4426836 - 1.7194581
Average (Standard dev.)-0.0024079666 (±0.04491872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.216 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened

Fileemd_27031_additional_1.map
AnnotationUnsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A

Fileemd_27031_half_map_1.map
AnnotationHalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_27031_half_map_2.map
AnnotationHalf B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : T32-15

EntireName: T32-15
Components
  • Complex: T32-15
    • Protein or peptide: T32-15-1
    • Protein or peptide: T32-15-2

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Supramolecule #1: T32-15

SupramoleculeName: T32-15 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: T32-15-1

MacromoleculeName: T32-15-1 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 49.525008 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DEAEEKARRV AEKVERLKRS GTSEDEIAEE VAREISEVIR TLKESGSSYE VIAEIVARIV AEIVEALKRS GTSEDEIAEI VARVISEVI RTLKESGSSY EVIAEIVARI VAEIVEALKR SGTSEDEIAE IVARVISEVI RTLKESGSSY EVIAEIVARI V AEIVEALK ...String:
DEAEEKARRV AEKVERLKRS GTSEDEIAEE VAREISEVIR TLKESGSSYE VIAEIVARIV AEIVEALKRS GTSEDEIAEI VARVISEVI RTLKESGSSY EVIAEIVARI VAEIVEALKR SGTSEDEIAE IVARVISEVI RTLKESGSSY EVIAEIVARI V AEIVEALK RSGTSEDEIA EIVARVISEV IRTLKESGSS AEVIAEIVAR IVAEIVEALK RSGTSEDEIA EIVARVISEV IR TLKESGS SSILIALIVA RIVAEIVEAL KRSGTSEDEI AEIVARVISE VIRTLKESGS SYEIIALIVA MIVAEIVRAL LRS GTSEEE IAKIVARVMN EVLRTLRESG SDFEVIREIL RLILAAIRAA LQKGGVSEDE IMRIEIKILL MLLRLSTAEL ERAT RSLKA ITEELKKNPS EDALVEHNRA IVEHNRIIVF NNILIALVLE AIVRAI

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Macromolecule #2: T32-15-2

MacromoleculeName: T32-15-2 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.066595 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TRTEIIRELE RSLREQEELA KRLMELLLKL LRLQMTGSSD EDVRRLMLRI IELVEEIEEL AREQKYLVEE LKRQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5.3 mg/mL
BufferpH: 8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab initio
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 511464

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