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- EMDB-42031: Computational Designed Nanocage O43_129_+8 -

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Basic information

Entry
Database: EMDB / ID: EMD-42031
TitleComputational Designed Nanocage O43_129_+8
Map data
Sample
  • Complex: O43-129_+8
    • Other: Cage_O43_129_A
    • Other: cage_O43_129_+8_B
KeywordsO43_129_+8 / O43 / 129+2 / 129_+8 / 129 / De Novo Nanocage / DE NOVO PROTEIN
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.98 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
DepositionSep 18, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42031.png

Downloads & links

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Map

FileDownload / File: emd_42031.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.89 Å
Density
Contour LevelBy AUTHOR: 0.332
Minimum - Maximum-0.18357597 - 0.6999366
Average (Standard dev.)-0.0003517776 (±0.04540126)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 338.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42031_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42031_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : O43-129_+8

EntireName: O43-129_+8
Components
  • Complex: O43-129_+8
    • Other: Cage_O43_129_A
    • Other: cage_O43_129_+8_B

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Supramolecule #1: O43-129_+8

SupramoleculeName: O43-129_+8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: A and B chains were expressed separately in e coli. 4 copies of chain A form a side. 3 copies of chain B form a side. The lysate of both expressions are mixed together. 8 sides of each come ...Details: A and B chains were expressed separately in e coli. 4 copies of chain A form a side. 3 copies of chain B form a side. The lysate of both expressions are mixed together. 8 sides of each come together to form a nanoparticle. The nanoparticle is purified by a HIS tag on chain A
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 2.186 MDa

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Macromolecule #1: Cage_O43_129_A

MacromoleculeName: Cage_O43_129_A / type: other / ID: 1 / Classification: other
Source (natural)Organism: unidentified (others)
SequenceString: mGCDAIQAAA ALGEAGISSN EILELLAAAA ELGLDPDAIQ AAAQLGEAGI SSEEIKELLR AAHELGLDPD AIAAAADLGQ AGVSPVEILA LLIAASVLGL DPDAIQAAAA LGEAGISAEE IIELLTAARD LGLDPDAIQA AAQLGEAGIS SEEIKELLRA AHELGLDPDC ...String:
mGCDAIQAAA ALGEAGISSN EILELLAAAA ELGLDPDAIQ AAAQLGEAGI SSEEIKELLR AAHELGLDPD AIAAAADLGQ AGVSPVEILA LLIAASVLGL DPDAIQAAAA LGEAGISAEE IIELLTAARD LGLDPDAIQA AAQLGEAGIS SEEIKELLRA AHELGLDPDC IAAAADLGQA GISSSEITAL LLAAAAIELA KRADDKDVRE IVRDALELAS RSTNDEVIRL ALEAAVLAAR STDSDVLEIV KDALELAKQS TNEEVIKLAL KAAVLAAKST DEEVLEEVKE ALRRAKESTD EEEIKEELRK AVEEAEGGSW lehhhhhh
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: cage_O43_129_+8_B

MacromoleculeName: cage_O43_129_+8_B / type: other / ID: 2 / Classification: other
Source (natural)Organism: unidentified (others)
SequenceString: mGDDLLLKLL ELLVEQARVS AEFARRQGDE KMLEEVARKA EEVARKAEEI ARKARKEGNL ELALKALEIL VRAAHVLAEI ARERGNEELQ KKAHKLAKEA LRQVIEIAIR AIQEGNLELA IIALHISVRI AEVLLETRPD DREEIREQQA IFELLIAALE AAIRLEKLKE ...String:
mGDDLLLKLL ELLVEQARVS AEFARRQGDE KMLEEVARKA EEVARKAEEI ARKARKEGNL ELALKALEIL VRAAHVLAEI ARERGNEELQ KKAHKLAKEA LRQVIEIAIR AIQEGNLELA IIALHISVRI AEVLLETRPD DREEIREQQA IFELLIAALE AAIRLEKLKE EGAPPEQIER VAEHGLERLK EIAKEISKEV DSPESKRIAY KIVAAAAEFL LKILAEGGAT PEQLERVTEH ALEVLKEVAK ELADSPESVR EAVRLISKLT QEGLKQLKEI GAPPEQIERV AEHGLEVLKE IAKYGSKLTD SPELKRELYR IISETAKELL KILAEGGATP EQLERVTKHA LEVLKEVAKE LADSPESVRE AVRLISKLTQ EGLKQLKEIG APPEQIERVA EHGLEVLKEI AKYGSKLTDS PELKRELYRI ISETAKELLK ILAEGGATPE QLERVTKHAL EVLKEVAKEL ADSPESGLAA LAAIASLAKL GLEQLKEIGA PPEQQRRVTK AGIEAVREIY RYGRKLY
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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 - Concentration: 300.0 mM / Component - Formula: NaClSodium chloride / Component - Name: sodium chloride / Details: 25mM Tris, 300mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 5.0 sec. / Average electron dose: 50.0 e/Å2

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Image processing

Particle selectionNumber selected: 8271 / Details: Particles were picked manually
Startup modelType of model: INSILICO MODEL / In silico model: Ab Initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 9 / Avg.num./class: 602 / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 12.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 5420
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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