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- EMDB-42944: Computational Designed Nanocage O43_129_+4 -

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Basic information

Entry
Database: EMDB / ID: EMD-42944
TitleComputational Designed Nanocage O43_129_+4
Map datadeepEMhancer sharpened map
Sample
  • Complex: Computational Designed Nanocage O43_129_+4
    • Protein or peptide: O43_129_+4 component A
    • Protein or peptide: O43_129_+4 component B
KeywordsO43 / Nanocage / De Novo / Programmable Design / DE NOVO PROTEIN
Biological speciesunidentified (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsCarr KD / Weidle C / Borst AJ
Funding support United States, 1 items
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, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42944.png

Downloads & links

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Map

FileDownload / File: emd_42944.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer sharpened map
Voxel sizeX=Y=Z: 1.86667 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.008993997 - 1.4493802
Average (Standard dev.)0.00102843 (±0.022722438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 672.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_42944_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_42944_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_42944_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Computational Designed Nanocage O43_129_+4

EntireName: Computational Designed Nanocage O43_129_+4
Components
  • Complex: Computational Designed Nanocage O43_129_+4
    • Protein or peptide: O43_129_+4 component A
    • Protein or peptide: O43_129_+4 component B

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Supramolecule #1: Computational Designed Nanocage O43_129_+4

SupramoleculeName: Computational Designed Nanocage O43_129_+4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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.
Source (natural)Organism: unidentified (others)

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Macromolecule #1: O43_129_+4 component A

MacromoleculeName: O43_129_+4 component A / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 33.976965 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGCDAIQAAA ALGEAGISSN EILELLAAAA ELGLDPDAIQ AAAQLGEAGI SSEEIKELLR AAHELGLDPD AIAAAADLGQ AGVSPVEIL ALLIAASVLG LDPDAIQAAA ALGEAGISAE EIIELLTAAR DLGLDPDAIQ AAAQLGEAGI SSEEIKELLR A AHELGLDP ...String:
MGCDAIQAAA ALGEAGISSN EILELLAAAA ELGLDPDAIQ AAAQLGEAGI SSEEIKELLR AAHELGLDPD AIAAAADLGQ AGVSPVEIL ALLIAASVLG LDPDAIQAAA ALGEAGISAE EIIELLTAAR DLGLDPDAIQ AAAQLGEAGI SSEEIKELLR A AHELGLDP DCIAAAADLG QAGISSSEIT ALLLAAAAIE LAKRADDKDV REIVRDALEL ASRSTNDEVI RLALEAAVLA AR STDSDVL EIVKDALELA KQSTNEEVIK LALKAAVLAA KSTDEEVLEE VKEALRRAKE STDEEEIKEE LRKAVEEAEG GSW LEHHHH HH

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Macromolecule #2: O43_129_+4 component B

MacromoleculeName: O43_129_+4 component B / type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.675922 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGDDLLLKLL ELLVEQARVS AEFARRQGDE KMLEEVARKA EEVARKAEEI ARKARKEGNL ELALKALEIL VRAAHVLAEI ARERGNEEL QKKAHKLAKE ALRQVIEIAI RAIQEGNLEL AIIALHISVR IAEVLLETRP DDREEIREQQ AIFELLIAAL E AAIRLEKL ...String:
MGDDLLLKLL ELLVEQARVS AEFARRQGDE KMLEEVARKA EEVARKAEEI ARKARKEGNL ELALKALEIL VRAAHVLAEI ARERGNEEL QKKAHKLAKE ALRQVIEIAI RAIQEGNLEL AIIALHISVR IAEVLLETRP DDREEIREQQ AIFELLIAAL E AAIRLEKL KEEGAPPEQI ERVAEHGLER LKEIAKEISK EVDSPESKRI AYKIVAAAAE FLLKILAEGG ATPEQLERVT EH ALEVLKE VAKELADSPE SVREAVRLIS KLTQEGLKQL KEIGAPPEQI ERVAEHGLEV LKEIAKYGSK LTDSPELKRE LYR IISETA KELLKILAEG GATPEQLERV TKHALEVLKE VAKELADSPE SGLAALAAIA SLAKLGLEQL KEIGAPPEQQ RRVT KAGIE AVREIYRYGR KLY

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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

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
300.0 mMNaClSodium chlorideSodium Chloride
25.0 mMtrisHClTRIS

Details: 300mM NaCl, 25mM Tris-HCL
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 23522
Startup modelType of model: INSILICO MODEL / In silico model: ab-initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final 3D classificationNumber classes: 8 / Avg.num./class: 2110 / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 16878
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsComputationally 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.
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 804.6 / Target criteria: Cross-correlation coefficient
Output model

PDB-8v3b:
Computational Designed Nanocage O43_129_+4

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