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- EMDB-39006: Focused refinement map of U5 Sm ring region of the human minor pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-39006
TitleFocused refinement map of U5 Sm ring region of the human minor pre-B complex
Map data
Sample
  • Complex: human minor pre-B complex
Keywordsspliceosome / minor spliceosome / U11 snRNP / U12 snRNP / U4atac / U6atac / CENATAC / TXNL4B / U11 snRNA / minor tri-snRNP / U12-type intron / SPLICING
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsBai R / Yuan M / Zhang P / Luo T / Shi Y / Wan R
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171214 China
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)32100987 China
CitationJournal: Science / Year: 2024
Title: Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome.
Authors: Rui Bai / Meng Yuan / Pu Zhang / Ting Luo / Yigong Shi / Ruixue Wan /
Abstract: The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we ...The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we report the 3.3-angstrom cryo-electron microscopy structure of the fully assembled human minor spliceosome pre-B complex. The atomic model includes U11 small nuclear ribonucleoprotein (snRNP), U12 snRNP, and U4atac/U6atac.U5 tri-snRNP. U11 snRNA is recognized by five U11-specific proteins (20K, 25K, 35K, 48K, and 59K) and the heptameric Sm ring. The 3' half of the 5'-splice site forms a duplex with U11 snRNA; the 5' half is recognized by U11-35K, U11-48K, and U11 snRNA. Two proteins, CENATAC and DIM2/TXNL4B, specifically associate with the minor tri-snRNP. A structural analysis uncovered how two conformationally similar tri-snRNPs are differentiated by the minor and major prespliceosomes for assembly.
History
DepositionFeb 3, 2024-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39006.png

Downloads & links

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Map

FileDownload / File: emd_39006.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 549.99 Å		1.07 Å/pix.
x 512 pix.
= 549.99 Å		1.07 Å/pix.
x 512 pix.
= 549.99 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.3746252 - 4.1125064
Average (Standard dev.)0.0038425599 (±0.04679445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 549.9904 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39006_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_39006_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 : human minor pre-B complex

EntireName: human minor pre-B complex
Components
  • Complex: human minor pre-B complex

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Supramolecule #1: human minor pre-B complex

SupramoleculeName: human minor pre-B complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.8 MDa

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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: 7.9
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
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: 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: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 388888
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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