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- EMDB-75763: Cryo-EM determined structure of designed nanoparticle O43-TM -

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Basic information

Entry
Database: EMDB / ID: EMD-75763
TitleCryo-EM determined structure of designed nanoparticle O43-TM
Map dataGlobal Refinement Map with Auto-sharpening
Sample
  • Complex: two component de novo designed nanoparticle with trans-membrane domain O43-TM
    • Protein or peptide: Designed nanoparticle O43-TM
    • Protein or peptide: Designed nanoparticle O43-B
KeywordsDe Novo / Membrane / Hydrophobic / Designed / Two Component / Octahedral / Micelle / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsCarr KD / Borst AJ / Weidle C
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-043758 United States
Bill & Melinda Gates FoundationINV-010680 United States
CitationJournal: To Be Published
Title: De Novo computational design and purification of two-component transmembrane nanoparticles
Authors: Zambrano DD
History
DepositionFeb 27, 2026-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75763.png

Downloads & links

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Map

FileDownload / File: emd_75763.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal Refinement Map with Auto-sharpening
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 600 pix.
= 504. Å		0.84 Å/pix.
x 600 pix.
= 504. Å		0.84 Å/pix.
x 600 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.20697978 - 0.4807076
Average (Standard dev.)0.00076612947 (±0.0112169925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 503.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Global Refinement Map sharpened using DeepEMhancer

Fileemd_75763_additional_1.map
AnnotationGlobal Refinement Map sharpened using DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Global Refinement Map without sharpening

Fileemd_75763_additional_2.map
AnnotationGlobal Refinement Map without sharpening
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local Refinement Half Map B

Fileemd_75763_additional_3.map
AnnotationLocal Refinement Half Map B
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: Local Refinement Half Map A

Fileemd_75763_additional_4.map
AnnotationLocal Refinement Half Map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local Refinement Map with Auto-sharpening

Fileemd_75763_additional_5.map
AnnotationLocal Refinement Map with Auto-sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local Refinement Map without sharpening

Fileemd_75763_additional_6.map
AnnotationLocal Refinement Map without sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Global Refinement Half Map A

Fileemd_75763_half_map_1.map
AnnotationGlobal Refinement Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Global Refinement Half Map B

Fileemd_75763_half_map_2.map
AnnotationGlobal Refinement Half 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 : two component de novo designed nanoparticle with trans-membrane d...

EntireName: two component de novo designed nanoparticle with trans-membrane domain O43-TM
Components
  • Complex: two component de novo designed nanoparticle with trans-membrane domain O43-TM
    • Protein or peptide: Designed nanoparticle O43-TM
    • Protein or peptide: Designed nanoparticle O43-B

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Supramolecule #1: two component de novo designed nanoparticle with trans-membrane d...

SupramoleculeName: two component de novo designed nanoparticle with trans-membrane domain O43-TM
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Designed two-component protein assembly with octahedral symmetry displaying a trans-membrane domain.
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.180 MDa

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Macromolecule #1: Designed nanoparticle O43-TM

MacromoleculeName: Designed nanoparticle O43-TM / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.10125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SKDTEDSRKI WRTIMLLLVF AILLSAIIWY QITTNPDTSQ IATLLSMQLL LIALMLVVIA LLLSRQTEQV AESIRRDVSA LAYVMLGLL LSLLNRLSLA AEAYKKAIEL DPNDALAWLL LGSVLEKLKR LDEAAEAYKK AIELKPNDAS AWKELGKVLE K LGRLDEAA ...String:
SKDTEDSRKI WRTIMLLLVF AILLSAIIWY QITTNPDTSQ IATLLSMQLL LIALMLVVIA LLLSRQTEQV AESIRRDVSA LAYVMLGLL LSLLNRLSLA AEAYKKAIEL DPNDALAWLL LGSVLEKLKR LDEAAEAYKK AIELKPNDAS AWKELGKVLE K LGRLDEAA DAYAEALRLD PDDTEAWKEL GKVLEKLGME EAAAMAKKAA KLLDPNDGSL EHHHHHH

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Macromolecule #2: Designed nanoparticle O43-B

MacromoleculeName: Designed nanoparticle O43-B / type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.244084 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEELFKKHKI VAVLRANSVE EAKEKAQAVF EGGVHLIEIT FTVPDADTVI KELSKLKEKG AIIGAGTVTS VEQCRKAVES GAEFIVSPH LDEEISQFCK EKGVFYMPGV MTPTELVKAM KLGHTILKLF PGEVVGPQFV KAMKGPFPNV KFVPTGGVDL D NVCEWFKA ...String:
MEELFKKHKI VAVLRANSVE EAKEKAQAVF EGGVHLIEIT FTVPDADTVI KELSKLKEKG AIIGAGTVTS VEQCRKAVES GAEFIVSPH LDEEISQFCK EKGVFYMPGV MTPTELVKAM KLGHTILKLF PGEVVGPQFV KAMKGPFPNV KFVPTGGVDL D NVCEWFKA GVLAVGVGEA LVDGEPRAVK IAAIAFRAVI KGCGCTEGSL EHHHHHH

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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

Concentration0.3 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 40 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Details: Wait time: 7.5 seconds Blot time: 0.5 seconds Blot force: 0 seconds.
DetailsParticles were imaged in two datasets. The first was heterogeneous and contamined both the designed nanoparticle assembly and a co-eluting contaminant protein. The second was almost completely pure with very little contaminant protein present.

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Digitization - Dimensions - Width: 5760 pixel / #0 - Digitization - Dimensions - Height: 4092 pixel / #0 - Number grids imaged: 1 / #0 - Number real images: 6211 / #0 - Average exposure time: 5.0 sec. / #0 - Average electron dose: 47.0 e/Å2 / #0 - Details: first dataset / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Digitization - Dimensions - Width: 5760 pixel / #1 - Digitization - Dimensions - Height: 4092 pixel / #1 - Number real images: 6887 / #1 - Average electron dose: 47.32 e/Å2 / #1 - Details: second dataset
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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

Image recording ID1
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: ab-initio
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF
Software:
Namedetails
cryoSPARC (ver. 4.4.1)global refinement
cryoSPARC (ver. 4.6.0)local refinement

Number images used: 42340
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4.1)
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: Computationally designed model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 163.2 / Target criteria: Cross-correlation coefficient
Output model

PDB-11kc:
Cryo-EM determined structure of designed nanoparticle O43-TM

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