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- EMDB-33039: Cryo-EM structure of a Group II Intron Complexed with its Reverse... -

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Basic information

Entry
Database: EMDB / ID: EMD-33039
TitleCryo-EM structure of a Group II Intron Complexed with its Reverse Transcriptase
Map data
Sample
  • Complex: Cryo-EM structure of a spliced group II intron RNP
Function / homology
Function and homology information


intron homing / RNA-directed DNA polymerase / mRNA processing / RNA-directed DNA polymerase activity / endonuclease activity / Hydrolases; Acting on ester bonds
Similarity search - Function
Domain X / : / Type II intron maturase / AI2M/AI1M-like, HNH endonuclease / : / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Group II intron-encoded protein LtrA
Similarity search - Component
Biological speciesLactococcus cremoris (lactic acid bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu N / Dong XL / Qu GS / Wang J / Wang HW / Belfort M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Functionalized graphene grids with various charges for single-particle cryo-EM
Authors: Lu Y / Liu N / Liu Y / Zheng L / Yang J / Wang J / Jia X / Zi Q / Peng H / Rao Y / Wang HW
History
DepositionMar 9, 2022-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33039.png

Downloads & links

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Map

FileDownload / File: emd_33039.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 256 pix.
= 248.32 Å		0.97 Å/pix.
x 256 pix.
= 248.32 Å		0.97 Å/pix.
x 256 pix.
= 248.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0124
Minimum - Maximum-0.048640057 - 0.09662974
Average (Standard dev.)0.00027433215 (±0.0023853001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 248.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33039_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33039_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_33039_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 a spliced group II intron RNP

EntireName: Cryo-EM structure of a spliced group II intron RNP
Components
  • Complex: Cryo-EM structure of a spliced group II intron RNP

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Supramolecule #1: Cryo-EM structure of a spliced group II intron RNP

SupramoleculeName: Cryo-EM structure of a spliced group II intron RNP / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Lactococcus cremoris (lactic acid bacteria)

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3333

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 399660
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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