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- EMDB-33426: Misfolded Tetrahymena ribozyme conformation 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-33426
TitleMisfolded Tetrahymena ribozyme conformation 2
Map dataCryo-EM structure of misfolded Tetrahymena ribozyme conformation 2 --- unsharpen
Sample
  • Complex: Misfolded Tetrahymena ribozyme conformation 2
    • RNA: RNA (388-MER)
KeywordsMisfolded Tetrahymena Ribozyme / Topological Crossing / Cryo-EM / refolding / RNA
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsLi S / Palo M / Pintilie G / Zhang X / Su Z / Kappel K / Chiu W / Zhang K / Das R
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129541 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122579 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21 AI145647 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Topological crossing in the misfolded ribozyme resolved by cryo-EM.
Authors: Shanshan Li / Michael Z Palo / Grigore Pintilie / Xiaojing Zhang / Zhaoming Su / Kalli Kappel / Wah Chiu / Kaiming Zhang / Rhiju Das /
Abstract: The group I intron has been a key system in the understanding of RNA folding and misfolding. The molecule folds into a long-lived misfolded intermediate (M) , which has been known to form extensive ...The group I intron has been a key system in the understanding of RNA folding and misfolding. The molecule folds into a long-lived misfolded intermediate (M) , which has been known to form extensive native-like secondary and tertiary structures but is separated by an unknown kinetic barrier from the native state (N). Here, we used cryogenic electron microscopy (cryo-EM) to resolve misfolded structures of the L-21 ScaI ribozyme. Maps of three M substates (M1, M2, M3) and one N state were achieved from a single specimen with overall resolutions of 3.5 Å, 3.8 Å, 4.0 Å, and 3.0 Å, respectively. Comparisons of the structures reveal that all the M substates are highly similar to N, except for rotation of a core helix P7 that harbors the ribozyme's guanosine binding site and the crossing of the strands J7/3 and J8/7 that connect P7 to the other elements in the ribozyme core. This topological difference between the M substates and N state explains the failure of 5'-splice site substrate docking in M, supports a topological isomer model for the slow refolding of M to N due to a trapped strand crossing, and suggests pathways for M-to-N refolding.
History
DepositionMay 14, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33426.png

Downloads & links

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Map

FileDownload / File: emd_33426.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of misfolded Tetrahymena ribozyme conformation 2 --- unsharpen
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.41868705 - 1.3723421
Average (Standard dev.)0.007758516 (±0.0434834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM structure of misfolded Tetrahymena ribozyme conformation 2...

Fileemd_33426_additional_1.map
AnnotationCryo-EM structure of misfolded Tetrahymena ribozyme conformation 2 --- sharpen
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_33426_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Histogram

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Half map: Half map 2

Fileemd_33426_half_map_2.map
AnnotationHalf map 2
Projections & Slices
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Sample components

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Entire : Misfolded Tetrahymena ribozyme conformation 2

EntireName: Misfolded Tetrahymena ribozyme conformation 2
Components
  • Complex: Misfolded Tetrahymena ribozyme conformation 2
    • RNA: RNA (388-MER)

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Supramolecule #1: Misfolded Tetrahymena ribozyme conformation 2

SupramoleculeName: Misfolded Tetrahymena ribozyme conformation 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: RNA (388-MER)

MacromoleculeName: RNA (388-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 125.402945 KDa
SequenceString: GGAGGGAAAA GUUAUCAGGC AUGCACCUGG UAGCUAGUCU UUAAACCAAU AGAUUGCAUC GGUUUAAAAG GCAAGACCGU CAAAUUGCG GGAAAGGGGU CAACAGCCGU UCAGUACCAA GUCUCAGGGG AAACUUUGAG AUGGCCUUGC AAAGGGUAUG G UAAUAAGC ...String:
GGAGGGAAAA GUUAUCAGGC AUGCACCUGG UAGCUAGUCU UUAAACCAAU AGAUUGCAUC GGUUUAAAAG GCAAGACCGU CAAAUUGCG GGAAAGGGGU CAACAGCCGU UCAGUACCAA GUCUCAGGGG AAACUUUGAG AUGGCCUUGC AAAGGGUAUG G UAAUAAGC UGACGGACAU GGUCCUAACC ACGCAGCCAA GUCCUAAGUC AACAGAUCUU CUGUUGAUAU GGAUGCAGUU CA CAGACUA AAUGUCGGUC GGGGAAGAUG UAUUCUUCUC AUAAGAUAUA GUCGGACCUC UCCUUAAUGG GAGCUAGCGG AUG AAGUGA UGCAACACUG GAGCCGCUGG GAACUAAUUU GUAUGCGAAA GUAUAUUGAU UAGUUUUGGA GU

GENBANK: GENBANK: X54512.1

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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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 42382 / Average electron dose: 51.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10414332
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.3) / Number images used: 431156
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.3)

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