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- EMDB-35878: Cryo-EM structure of DIP-2I8I polymorph 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-35878
TitleCryo-EM structure of DIP-2I8I polymorph 2
Map data
Sample
  • Complex: Cryo-EM structue of DIP-2I8I fibril polymorph 2
    • Protein or peptide: GLY-PHI-GLY-ASN-GLY-ASN-GLY-PHI-GLY
KeywordsIodinated peptide / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsLi DN / Ma YY / Li D / Dai B / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of DIP-2I8I fibril polymorph 2
Authors: Li DN / Ma YY / Li D / Dai B / Liu C
History
DepositionApr 9, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35878.png

Downloads & links

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Map

FileDownload / File: emd_35878.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 416 pix.
= 345.28 Å		0.83 Å/pix.
x 416 pix.
= 345.28 Å		0.83 Å/pix.
x 416 pix.
= 345.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0057
Minimum - Maximum-0.012811633 - 0.028543148
Average (Standard dev.)0.0003302577 (±0.0016932294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 345.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35878_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35878_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 : Cryo-EM structue of DIP-2I8I fibril polymorph 2

EntireName: Cryo-EM structue of DIP-2I8I fibril polymorph 2
Components
  • Complex: Cryo-EM structue of DIP-2I8I fibril polymorph 2
    • Protein or peptide: GLY-PHI-GLY-ASN-GLY-ASN-GLY-PHI-GLY

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Supramolecule #1: Cryo-EM structue of DIP-2I8I fibril polymorph 2

SupramoleculeName: Cryo-EM structue of DIP-2I8I fibril polymorph 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GLY-PHI-GLY-ASN-GLY-ASN-GLY-PHI-GLY

MacromoleculeName: GLY-PHI-GLY-ASN-GLY-ASN-GLY-PHI-GLY / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.077621 KDa
SequenceString:
G(PHI)GNGNG(PHI)G

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.83 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.21 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11823
FSC plot (resolution estimation)

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