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- EMDB-71961: Cryo-EM structure of designed Orb2 amyloid (LVLVF; polymorph 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-71961
TitleCryo-EM structure of designed Orb2 amyloid (LVLVF; polymorph 1)
Map dataLVLVF (Mut3)-Orb2 Map
Sample
  • Complex: Cryo-EM structure of designed Orb2 amyloid (LVLVF; polymorph 1)
    • Protein or peptide: Designed Orb2 Amyloid Core
KeywordsPolymorph1 / Recombinant Protein / Orb2 Amyloid Core / Designed Mutants / PROTEIN FIBRIL
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSingh R / Joachimiak L / Si K / Kaili L
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg InitiativeCP2-1-0000000296 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of designed Orb2 amyloid (LVLVF, polymorph 1)
Authors: Singh R / Joachimiak L
History
DepositionAug 5, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71961.png

Downloads & links

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Map

FileDownload / File: emd_71961.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLVLVF (Mut3)-Orb2 Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 300 pix.
= 280.8 Å		0.94 Å/pix.
x 300 pix.
= 280.8 Å		0.94 Å/pix.
x 300 pix.
= 280.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.936 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.62
Minimum - Maximum-17.928816000000001 - 22.718830000000001
Average (Standard dev.)0.0033848814 (±0.37144497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 280.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71961_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: LVLVF (Mut3)-Orb2 Map

Fileemd_71961_additional_1.map
AnnotationLVLVF (Mut3)-Orb2 Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: LVLVF (Mut3)-Orb2 Postprocessed Map

Fileemd_71961_additional_2.map
AnnotationLVLVF (Mut3)-Orb2 Postprocessed Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: LVLVF (Mut3)-Orb2 Postprocessed Masked Map

Fileemd_71961_additional_3.map
AnnotationLVLVF (Mut3)-Orb2 Postprocessed Masked Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: LVLVF (Mut3)-Orb2 Half Map

Fileemd_71961_half_map_1.map
AnnotationLVLVF (Mut3)-Orb2 Half Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: LVLVF (Mut3)-Orb2 Half Map

Fileemd_71961_half_map_2.map
AnnotationLVLVF (Mut3)-Orb2 Half 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 : Cryo-EM structure of designed Orb2 amyloid (LVLVF; polymorph 1)

EntireName: Cryo-EM structure of designed Orb2 amyloid (LVLVF; polymorph 1)
Components
  • Complex: Cryo-EM structure of designed Orb2 amyloid (LVLVF; polymorph 1)
    • Protein or peptide: Designed Orb2 Amyloid Core

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Supramolecule #1: Cryo-EM structure of designed Orb2 amyloid (LVLVF; polymorph 1)

SupramoleculeName: Cryo-EM structure of designed Orb2 amyloid (LVLVF; polymorph 1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Orb2 Amyloid peptide are chemically synthesized.
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 4 kDa/nm

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Macromolecule #1: Designed Orb2 Amyloid Core

MacromoleculeName: Designed Orb2 Amyloid Core / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 3.920249 KDa
SequenceString:
QLHQQQHQQQ HLQHVQHLQQ VQFHQHQQQL S

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.15
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
75.0 mMNaClSodium Chloride
20.0 mg/mlC3H8O3Glycerol
2.0 mMMgCl2Magnesium Chloride
10.0 mMKClPotassium Chloride

Details: 10mM HEPES, 75mM NaCl, 2% glycerol, 2mM MgCl2, 10mM KCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.00038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification Carried out in liquid Nitrogen atmosphere.
DetailsHomogenous

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 5994 / Average exposure time: 6.25 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 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: 2.4 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2713980
CTF correctionSoftware - Name: CTFFIND / Software - details: GUI / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: The initial model was generated from 2D class averages using the relion_helix_inimodel2d program in RELION. This model was used to generate initial projections for 3D refinement of the helical structure.
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta-1-commit-b75b38) / Number images used: 58092
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 5.0-beta-1-commit-b75b38)
Details: Initial angles were assigned based on helical symmetry using relion_helix_inimodel2d
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta-1-commit-b75b38)
Details: Final orientations of particles were assigned using Bayesian maximum likelihood refinement implemented in Relion.
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 5.0-beta-1-commit-b75b38)
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: Initial model generated automatically using ModelAngelo from the experimental cryo-EM map. Model was further manually inspected and refined using Coot and Phenix.
DetailsInitial model fitting was performed using Coot and Phenix, with final adjustments completed in ChimeraX.
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 5817 / Target criteria: Cross Correlation Coefficient
Output model

PDB-9px8:
Cryo-EM structure of designed Orb2 amyloid (LVLVF, polymorph 1)

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