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- EMDB-40926: CryoEM Structure of Computationally Designed Nanocage O32-ZL4 -

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Basic information

Entry
Database: EMDB / ID: EMD-40926
TitleCryoEM Structure of Computationally Designed Nanocage O32-ZL4
Map data
Sample
  • Complex: O32-ZL4
    • Protein or peptide: O32-ZL4 Component A
    • Protein or peptide: O32-ZL4 Component B
  • Ligand: SODIUM ION
KeywordsO32-ZL4 / DE NOVO PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWeidle C / Borst A
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 30, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40926.png

Downloads & links

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Map

FileDownload / File: emd_40926.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 420 pix.
= 352.8 Å		0.84 Å/pix.
x 420 pix.
= 352.8 Å		0.84 Å/pix.
x 420 pix.
= 352.8 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.133
Minimum - Maximum-1.0959196 - 1.7260058
Average (Standard dev.)0.00067367894 (±0.057205386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 352.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_40926_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40926_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : O32-ZL4

EntireName: O32-ZL4
Components
  • Complex: O32-ZL4
    • Protein or peptide: O32-ZL4 Component A
    • Protein or peptide: O32-ZL4 Component B
  • Ligand: SODIUM ION

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Supramolecule #1: O32-ZL4

SupramoleculeName: O32-ZL4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 764.91792 KDa

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Macromolecule #1: O32-ZL4 Component A

MacromoleculeName: O32-ZL4 Component A / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.766459 KDa
SequenceString:
MTDELLRLAK EQAELLKEIK ILVELIAMLV KVIQKDPSDE ALKALAELVR KLKELVEDME RSMKEQLYII KGSWSG

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Macromolecule #2: O32-ZL4 Component B

MacromoleculeName: O32-ZL4 Component B / type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 23.170152 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKMEELFKKH KIVAVLRAND AQEAREKALA VFEGGVHLIE ITFTVPNAAA VILLLSFLKE KGAIIGAGTV TSEEQCALAV LSGAEFIVS PHLDEEISQF CKEKGVFYMP GVMTPTELVK AMKLGHTILK LFPGEVVGPQ FVKAMKGPFP NVKFVPTGGV N LDNVCEWF ...String:
MKMEELFKKH KIVAVLRAND AQEAREKALA VFEGGVHLIE ITFTVPNAAA VILLLSFLKE KGAIIGAGTV TSEEQCALAV LSGAEFIVS PHLDEEISQF CKEKGVFYMP GVMTPTELVK AMKLGHTILK LFPGEVVGPQ FVKAMKGPFP NVKFVPTGGV N LDNVCEWF KAGVLAVGVG SALVKGTPDE VREKAKAFVE KIRGCTELEH HHHHH

UniProtKB: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 24
Molecular weightTheoretical: 22.99 Da

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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

Concentration2.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3HClTris HCl pH 7.5
150.0 mMNaClSodium Chloride

Details: 25 mM Tris/HCl pH 7.5, 150 mM NaCl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.0001 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details25 mM Tris, 150 mM NaCl

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 673044
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 674044
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Computational model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 144.9 / Target criteria: Cross-correlation coefficient
Output model

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

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