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- EMDB-29974: Cryo-EM structure of synthetic tetrameric building block sC4 -

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Basic information

Entry
Database: EMDB / ID: EMD-29974
TitleCryo-EM structure of synthetic tetrameric building block sC4
Map data
Sample
  • Complex: De novo designed tetramer sC4
    • Protein or peptide: sC4
Keywordssynthetic / tetramer / self-assembling / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsRedler RL / Huddy TF / Hsia Y / Baker D / Ekiert D / Bhabha G
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private 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
DepositionMar 7, 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_29974.png

Downloads & links

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Map

FileDownload / File: emd_29974.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.0266
Minimum - Maximum-0.060537156 - 0.09936816
Average (Standard dev.)0.0000021774092 (±0.0045735636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29974_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_29974_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : De novo designed tetramer sC4

EntireName: De novo designed tetramer sC4
Components
  • Complex: De novo designed tetramer sC4
    • Protein or peptide: sC4

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Supramolecule #1: De novo designed tetramer sC4

SupramoleculeName: De novo designed tetramer sC4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: sC4

MacromoleculeName: sC4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 57.826109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSGHHHHHH GSGSSEKALE ILREALKELE DIAKEQRKIL KDALDELREE AEKLREDGND EEEINKRLNE LMKIAVEALE LTIEVLRSL AESALRALEL LLKLAEDHKV IEEAVKLLLE FLKKLAEVAE EANRLALEFL EELIELGGDV EAAAKASKEA A RASAEFAR ...String:
MGSGHHHHHH GSGSSEKALE ILREALKELE DIAKEQRKIL KDALDELREE AEKLREDGND EEEINKRLNE LMKIAVEALE LTIEVLRSL AESALRALEL LLKLAEDHKV IEEAVKLLLE FLKKLAEVAE EANRLALEFL EELIELGGDV EAAAKASKEA A RASAEFAR AIVEILEEVA RLAIEFIEDE KLLARIAQLI IKAITEIVRI MAEMASLNVK AMSEIIKLAD DETAKKAVKI AL EILEMAM KVAEEANEAA LRVLELAVKA GGDVELAAEA SHELAKASLE VLKIMVEAAE LLARAAIEVI EDEKLLAEAA QLV IEAIRR LMEIMARIAK LNAEFLARVM KLADEETAER VLEIITEILR QASELAEEAN KAAERVLDLA RKAGGDEELV HTAS SLLIK ASAEVLRILF EAAVHAILAF NEVLYRLLKE AGADEEFLKE IEIKLAEIEM KALVAKNKLE SILSAIDMKA KRGAS EEEL KELLRELKKT VEDMLRELER LSEESRRIAE KARKT

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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
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: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: blot time = 4s.

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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: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Slit width: 30 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3850 / Average exposure time: 1.6 sec. / Average electron dose: 47.07 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3781336
Startup modelType of model: NONE / Details: Ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5 / Avg.num./class: 242431 / Software - Name: RELION (ver. 3.0) / Details: C1
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 378829

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 224.3
Output model

PDB-8gel:
Cryo-EM structure of synthetic tetrameric building block sC4

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