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- EMDB-49307: Cryo-EM of NBD-L4pY filament at 5mM concentration -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49307
TitleCryo-EM of NBD-L4pY filament at 5mM concentration
Map datafull map
Sample
  • Complex: (UQ4)LLLL(PTR)
    • Protein or peptide: (UQ4)LLLL(PTR)
Keywordspeptide fiber / helical polymer / protein fibril
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZia A / Guo J / Xu B / Wang F
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA142746 United States
CitationJournal: To Be Published
Title: Cryo-EM of NBD-L4pY filament at 5mM concentration
Authors: Zia A / Guo J / Xu B / Wang F
History
DepositionFeb 19, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49307.png

Downloads & links

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Map

FileDownload / File: emd_49307.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.55
Minimum - Maximum-0.042394873 - 9.698744
Average (Standard dev.)0.25767374 (±0.99921656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_49307_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_49307_half_map_2.map
Annotationhalf 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 : (UQ4)LLLL(PTR)

EntireName: (UQ4)LLLL(PTR)
Components
  • Complex: (UQ4)LLLL(PTR)
    • Protein or peptide: (UQ4)LLLL(PTR)

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Supramolecule #1: (UQ4)LLLL(PTR)

SupramoleculeName: (UQ4)LLLL(PTR) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: (UQ4)LLLL(PTR)

MacromoleculeName: (UQ4)LLLL(PTR) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 947.968 Da
SequenceString:
(UQ4)LLLL(PTR)

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 0.39 Å
Applied symmetry - Helical parameters - Δ&Phi: 43.07 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 256561
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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