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- EMDB-39299: Human resource SGLT1-MAP17 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39299
TitleHuman resource SGLT1-MAP17 complex
Map data
Sample
  • Complex: SGLT1-MAP17
KeywordsComplex / MEMBRANE PROTEIN
Biological speciessantria sp sf9 (fall armyworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen L / Zhang XZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930069 China
CitationJournal: Sci Adv / Year: 2024
Title: Correction of preferred orientation-induced distortion in cryo-electron microscopy maps.
Authors: Dongjie Zhu / Weili Cao / Junxi Li / Chunling Wu / Duanfang Cao / Xinzheng Zhang /
Abstract: Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been ...Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been attempted to address this preferred orientation problem using tilt-collection strategy and modifications to grids or to air-water interfaces. However, these approaches often require time-consuming experiments, and the effect was always protein dependent. Here, we developed a procedure containing removing misaligned particles and an iterative reconstruction method based on signal-to-noise ratio of Fourier component to correct this distortion by recovering missing data using a purely computational algorithm. This procedure called signal-to-noise ratio iterative reconstruction method (SIRM) was applied on incomplete datasets of various proteins to fix distortion in cryo-EM maps and to a more isotropic resolution. In addition, SIRM provides a better reference map for further reconstruction refinements, resulting in an improved alignment, which ultimately improves map quality and benefits model building.
History
DepositionFeb 28, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39299.png

Downloads & links

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Map

FileDownload / File: emd_39299.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 200 pix.
= 233.4 Å		1.17 Å/pix.
x 200 pix.
= 233.4 Å		1.17 Å/pix.
x 200 pix.
= 233.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.167 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.75
Minimum - Maximum-4.665397 - 6.9760213
Average (Standard dev.)-0.0015769982 (±0.13953127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 233.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39299_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_39299_half_map_1.map
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Half map: #2

Fileemd_39299_half_map_2.map
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Sample components

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Entire : SGLT1-MAP17

EntireName: SGLT1-MAP17
Components
  • Complex: SGLT1-MAP17

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Supramolecule #1: SGLT1-MAP17

SupramoleculeName: SGLT1-MAP17 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: santria sp sf9 (fall armyworm)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 37.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

33962

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 280215
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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