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- EMDB-42906: Computational Designed Nanocage O43_129 -

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Basic information

Entry
Database: EMDB / ID: EMD-42906
TitleComputational Designed Nanocage O43_129
Map dataMain Map, DeepEMhancer
Sample
  • Complex: Nanocage O43_129
    • Protein or peptide: O43_129 component B
    • Protein or peptide: O43_129 component A
KeywordsDe Novo / Nanocage / O43_129 / extendable nanomaterials / DE NOVO PROTEIN
Biological speciesunidentified (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.77 Å
AuthorsWeidle C / Kibler RD
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 22, 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_42906.png

Downloads & links

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Map

FileDownload / File: emd_42906.map.gz / Format: CCP4 / Size: 620.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain Map, DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 546 pix.
= 483.21 Å		0.89 Å/pix.
x 546 pix.
= 483.21 Å		0.89 Å/pix.
x 546 pix.
= 483.21 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0378
Minimum - Maximum-0.005106043 - 1.566966
Average (Standard dev.)0.0022870116 (±0.03369293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions546546546
Spacing546546546
CellA=B=C: 483.21 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Homogeneous Refinement

Fileemd_42906_additional_1.map
AnnotationHomogeneous Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_42906_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_42906_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nanocage O43_129

EntireName: Nanocage O43_129
Components
  • Complex: Nanocage O43_129
    • Protein or peptide: O43_129 component B
    • Protein or peptide: O43_129 component A

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Supramolecule #1: Nanocage O43_129

SupramoleculeName: Nanocage O43_129 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Chain A and Chain B are expressed separately in E coli. Complex is formed by mixing the cell lysis of both expressions, forming the nanocage. Nanocage was purified through a His tag on chain A.
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 1.60 MDa

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Macromolecule #1: O43_129 component B

MacromoleculeName: O43_129 component B / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 34.478918 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGDDLLLKLL ELLVEQARVS AEFARRQGDE KMLEEVARKA EEVARKAESI ARKARKEGNL ELALKALEIL VRAAHVLAEI ARERGNEEL QKKAHKLAKE ALRQVIEIAI RAIQEGNLEL AIIALHISVR IAEVLLETRP DDREEIREQQ AIFELLIAAL E AAIRLEKL ...String:
MGDDLLLKLL ELLVEQARVS AEFARRQGDE KMLEEVARKA EEVARKAESI ARKARKEGNL ELALKALEIL VRAAHVLAEI ARERGNEEL QKKAHKLAKE ALRQVIEIAI RAIQEGNLEL AIIALHISVR IAEVLLETRP DDREEIREQQ AIFELLIAAL E AAIRLEKL KEEGAPPEQI ERVAEHGLER LKEIAKEISK EVDSPESKRI AYKIVAAAAE FLLKILAEGG ATPEQLERVT EH ALEVLKE VAKELADSPE SGLAALAAIA SLAKLGLEQL KEIGAPPEQQ RRVTKAGIEA VREIYRYGRK LY

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Macromolecule #2: O43_129 component A

MacromoleculeName: O43_129 component A / type: protein_or_peptide / ID: 2 / 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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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
25.0 mMTrisHClTris
300.0 mMNaClSodium Chloride

Details: 25mM Tris HCl, 300mM NaCl, pH 8
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 40928
Startup modelType of model: INSILICO MODEL / In silico model: Ab Initio Model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 13400
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Avg.num./class: 3352 / Software - Name: cryoSPARC
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: De Novo Design
DetailsModel was initially fit in Chimera. Model was further refined with Namdinator, Isolde, and Coot
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 955.4
Output model

PDB-8v2d:
Computational Designed Nanocage O43_129

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