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- EMDB-37072: Cryo-EM structure of dimeric ATP-TTR-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-37072
TitleCryo-EM structure of dimeric ATP-TTR-3
Map data
Sample
  • Complex: Cryo-EM structure of dimeric ATP-TTR-3
    • RNA: ATP-TTR-3
KeywordsATP stabilizer / cryo-EM / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.59 Å
AuthorsChen XY / Jia GW / Su ZM
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
Ministry of Science and Technology (MoST, China)2021YFA301900 China
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 China
CitationJournal: Nat Protoc / Year: 2025
Title: RNA sample optimization for cryo-EM analysis.
Authors: Xingyu Chen / Liu Wang / Jiahao Xie / Jakub S Nowak / Bingnan Luo / Chong Zhang / Guowen Jia / Jian Zou / Dingming Huang / Sebastian Glatt / Yang Yang / Zhaoming Su /
Abstract: RNAs play critical roles in most biological processes. Although the three-dimensional (3D) structures of RNAs primarily determine their functions, it remains challenging to experimentally determine ...RNAs play critical roles in most biological processes. Although the three-dimensional (3D) structures of RNAs primarily determine their functions, it remains challenging to experimentally determine these 3D structures due to their conformational heterogeneity and intrinsic dynamics. Cryogenic electron microscopy (cryo-EM) has recently played an emerging role in resolving dynamic conformational changes and understanding structure-function relationships of RNAs including ribozymes, riboswitches and bacterial and viral noncoding RNAs. A variety of methods and pipelines have been developed to facilitate cryo-EM structure determination of challenging RNA targets with small molecular weights at subnanometer to near-atomic resolutions. While a wide range of conditions have been used to prepare RNAs for cryo-EM analysis, correlations between the variables in these conditions and cryo-EM visualizations and reconstructions remain underexplored, which continue to hinder optimizations of RNA samples for high-resolution cryo-EM structure determination. Here we present a protocol that describes rigorous screenings and iterative optimizations of RNA preparation conditions that facilitate cryo-EM structure determination, supplemented by cryo-EM data processing pipelines that resolve RNA dynamics and conformational changes and RNA modeling algorithms that generate atomic coordinates based on moderate- to high-resolution cryo-EM density maps. The current protocol is designed for users with basic skills and experience in RNA biochemistry, cryo-EM and RNA modeling. The expected time to carry out this protocol may range from 3 days to more than 3 weeks, depending on the many variables described in the protocol. For particularly challenging RNA targets, this protocol could also serve as a starting point for further optimizations.
History
DepositionAug 4, 2023-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37072.png

Downloads & links

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Map

FileDownload / File: emd_37072.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 384 pix.
= 376.32 Å		0.98 Å/pix.
x 384 pix.
= 376.32 Å		0.98 Å/pix.
x 384 pix.
= 376.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.312
Minimum - Maximum-1.2553673 - 2.3926854
Average (Standard dev.)-0.00022765738 (±0.034244817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 376.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37072_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37072_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 structure of dimeric ATP-TTR-3

EntireName: Cryo-EM structure of dimeric ATP-TTR-3
Components
  • Complex: Cryo-EM structure of dimeric ATP-TTR-3
    • RNA: ATP-TTR-3

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Supramolecule #1: Cryo-EM structure of dimeric ATP-TTR-3

SupramoleculeName: Cryo-EM structure of dimeric ATP-TTR-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: ATP-TTR-3

MacromoleculeName: ATP-TTR-3 / type: rna / ID: 1
Source (natural)Organism: synthetic construct (others)
SequenceString:
GGCGAUAUGG CAUGGAAUCA GCUCAAGGAA CUGUGAACGU AUAUCGGGCA ACGACUAGGA AACUAGUCGU UGGGAAGAAA CUGCCGAUAU ACGGGAGUUC CUUGAGCGGG AGAUUCCAUG CCUAAGUCGC

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.99 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.978 µm / Nominal defocus min: 0.464 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61627
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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