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- PDB-9pzd: Cryo-EM structure of designed Orb2 amyloid (LVLVF, polymorph 2) -

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Basic information

Entry
Database: PDB / ID: 9pzd
TitleCryo-EM structure of designed Orb2 amyloid (LVLVF, polymorph 2)
ComponentsDesigned Orb2 Amyloid Core (LVLVF, Polymorph 2)
KeywordsPROTEIN FIBRIL / Polymorph 2 / Recombinant Protein / Orb2 Amyloid Core / Designed Mutants
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSingh, R. / Kaili, L. / Si, K. / Joachimiak, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Chan Zuckerberg InitiativeCP2-1-0000000296 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of designed Orb2 amyloid (LVLVF, polymorph 2)
Authors: Singh, R. / Kaili, L. / Si, K. / Joachimiak, L.
History
DepositionAug 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)
B: Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)
C: Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)
D: Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)
E: Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)
F: Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)
G: Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)
H: Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)
I: Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)
J: Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)


Theoretical massNumber of molelcules
Total (without water)39,20210
Polymers39,20210
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide
Designed Orb2 Amyloid Core (LVLVF, Polymorph 2)


Mass: 3920.249 Da / Num. of mol.: 10 / Source method: obtained synthetically / Details: Protofilament Assembly / Source: (synth.) Drosophila melanogaster (fruit fly)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM Structure of designed Orb2 amyloid (LVLVF; Polymorph 2)
Type: COMPLEX / Details: Orb2 Amyloid Peptide are chemically synthesized / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 4 kDa/nm / Experimental value: YES
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.15
Details: 10mM HEPES, 75Mm NaCl, 2% glycerol, 2mM MgCl2, 10mM KCl
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESC8H18N2O4S1
275 mMSodium ChlorideNaCl1
320 mg/mlGlycerolC3H8O31
42 mMMagnesium ChlorideMgCl21
510 mMPotassium ChlorideKCl1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Homogenous
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 291.15 K
Details: Vitrification Carried out in liquid Nitrogen atmosphere

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.25 sec. / Electron dose: 60 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5994
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1RELION5.0-Beta-1particle selectionGUI
2SerialEM4image acquisition
4CTFFINDCTF correctionGUI
7Coot0.9.8.96model fitting
9RELION5.0-beta-1-commit-b75b38initial Euler assignment
10RELION5.0-beta-1-commit-b75b38final Euler assignment
11RELION5.0-beta-1-commit-b75b38classification
12RELION5.0-beta-1-commit-b75b383D reconstruction
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2713980
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94083 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 3878 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross Correlation Coefficient
Details: Initial model fitting was performed using Coot and Phenix, with final adjustments completed in ChimeraX.
Atomic model buildingDetails: Initial model generated using ModelAngelo from the cryo-EM map.
Source name: Other / Type: in silico model

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