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- EMDB-24096: Continuous movement of the pre-catalytic spliceosome, mode 1+2. -

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Basic information

Entry
Database: EMDB / ID: EMD-24096
TitleContinuous movement of the pre-catalytic spliceosome, mode 1+2.
Map dataContinuous movement of the pre-catalytic spliceosome, mode 1 2.
Sample
  • Complex: Pre-catalytic spliceosome
Function / homology
Function and homology information


Sm-like protein family complex / spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / maturation of 5S rRNA / snoRNA guided rRNA 2'-O-methylation / Lsm1-7-Pat1 complex / U6 snRNP / box C/D sno(s)RNA 3'-end processing / deadenylation-dependent decapping of nuclear-transcribed mRNA ...Sm-like protein family complex / spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / maturation of 5S rRNA / snoRNA guided rRNA 2'-O-methylation / Lsm1-7-Pat1 complex / U6 snRNP / box C/D sno(s)RNA 3'-end processing / deadenylation-dependent decapping of nuclear-transcribed mRNA / generation of catalytic spliceosome for first transesterification step / box C/D methylation guide snoRNP complex / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / P-body assembly / sno(s)RNA-containing ribonucleoprotein complex / snRNP binding / small nuclear ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / poly(U) RNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U3 snoRNA binding / U1 snRNP / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / mRNA 5'-splice site recognition / nuclear-transcribed mRNA catabolic process / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / cellular response to glucose starvation / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / spliceosomal complex / P-body / mRNA splicing, via spliceosome / rRNA processing / metallopeptidase activity / nucleic acid binding / RNA helicase activity / RNA helicase / response to xenobiotic stimulus / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Pre-mRNA-splicing factor Prp9, N-terminal / Pre-mRNA-splicing factor PRP9 N-terminus / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / PRP38 family / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Sm-like protein Lsm8 ...Pre-mRNA-splicing factor Prp9, N-terminal / Pre-mRNA-splicing factor PRP9 N-terminus / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / PRP38 family / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Sm-like protein Lsm8 / U6 snRNA-associated Sm-like protein Lsm1/8 / Pre-mRNA processing factor 4 (PRP4)-like / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Splicing Factor Motif, present in Prp18 and Pr04 / Sm-like protein Lsm7 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / pre-mRNA processing factor 3 domain / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / PRP1 splicing factor, N-terminal / SF3A2 domain / : / PRP1 splicing factor, N-terminal / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / SF3B4, RNA recognition motif 1 / : / Splicing factor 3A subunit 1, conserved domain / Splicing factor 3A subunit 1 / Pre-mRNA splicing factor PRP21 like protein / : / : / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Zinc-finger of C2H2 type / PHF5-like / PHF5-like protein / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / H/ACA ribonucleoprotein complex, subunit Nhp2-like / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / PPP2R1A-like HEAT repeat / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / : / Leucine-rich repeat / Pre-mRNA-splicing factor Syf1-like / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Sec63 domain / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D3 / : / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm7/SmG
Similarity search - Domain/homology
U6 snRNA-associated Sm-like protein LSm6 / RDS3 complex subunit 10 / Pre-mRNA-splicing factor 6 / Pre-mRNA-splicing factor PRP9 / U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-splicing factor PRP21 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / U6 snRNA-associated Sm-like protein LSm2 ...U6 snRNA-associated Sm-like protein LSm6 / RDS3 complex subunit 10 / Pre-mRNA-splicing factor 6 / Pre-mRNA-splicing factor PRP9 / U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-splicing factor PRP21 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / U6 snRNA-associated Sm-like protein LSm2 / Pre-mRNA-splicing factor SPP381 / 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein B / U6 snRNA-associated Sm-like protein LSm4 / U6 snRNA-associated Sm-like protein LSm5 / Small nuclear ribonucleoprotein G / U2 small nuclear ribonucleoprotein B'' / Small nuclear ribonucleoprotein Sm D3 / U6 snRNA-associated Sm-like protein LSm8 / Pre-mRNA-processing factor 31 / U2 snRNP component HSH155 / U6 snRNA-associated Sm-like protein LSm7 / Small nuclear ribonucleoprotein F / U6 snRNA-associated Sm-like protein LSm3 / Pre-mRNA-splicing factor 38 / Small nuclear ribonucleoprotein Sm D1 / Cold sensitive U2 snRNA suppressor 1 / U4/U6 small nuclear ribonucleoprotein PRP3 / Pre-mRNA-splicing factor RSE1 / Small nuclear ribonucleoprotein Sm D2 / Spliceosomal protein DIB1 / Pre-mRNA-splicing factor RDS3 / Pre-mRNA-splicing factor PRP11 / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein E / 23 kDa U4/U6.U5 small nuclear ribonucleoprotein component / 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component / Protein HSH49
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsChen M / Ludtke SJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139 United States
CitationJournal: Nat Methods / Year: 2021
Title: Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM.
Authors: Muyuan Chen / Steven J Ludtke /
Abstract: Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual ...Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual macromolecules sampling different conformational and compositional states. While numerous methods are available for computational classification of discrete states, characterization of continuous conformational changes or large numbers of discrete state without human supervision remains challenging. Here we present e2gmm, a machine learning algorithm to determine a conformational landscape for proteins or complexes using a three-dimensional Gaussian mixture model mapped onto two-dimensional particle images in known orientations. Using a deep neural network architecture, e2gmm can automatically resolve the structural heterogeneity within the protein complex and map particles onto a small latent space describing conformational and compositional changes. This system presents a more intuitive and flexible representation than other manifold methods currently in use. We demonstrate this method on both simulated data and three biological systems to explore compositional and conformational changes at a range of scales. The software is distributed as part of EMAN2.
History
DepositionMay 24, 2021-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateAug 25, 2021-
Current statusAug 25, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24096.png

Downloads & links

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Map

FileDownload / File: emd_24096.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationContinuous movement of the pre-catalytic spliceosome, mode 1 2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.25 Å/pix.
x 128 pix.
= 543.68 Å		4.25 Å/pix.
x 128 pix.
= 543.68 Å		4.25 Å/pix.
x 128 pix.
= 543.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2475 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-15.939724 - 20.981684
Average (Standard dev.)0.014574862 (±0.93923527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 543.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24754.24754.2475
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z543.680543.680543.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-15.94020.9820.015

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Supplemental data

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Additional map: Continuous movement of the pre-catalytic spliceosome, mode 1...

Fileemd_24096_additional_1.map
AnnotationContinuous movement of the pre-catalytic spliceosome, mode 1 2, frame 5.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Continuous movement of the pre-catalytic spliceosome, mode 1...

Fileemd_24096_additional_2.map
AnnotationContinuous movement of the pre-catalytic spliceosome, mode 1 2, frame 4.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Continuous movement of the pre-catalytic spliceosome, mode 1...

Fileemd_24096_additional_3.map
AnnotationContinuous movement of the pre-catalytic spliceosome, mode 1 2, frame 3.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Continuous movement of the pre-catalytic spliceosome, mode 1...

Fileemd_24096_additional_4.map
AnnotationContinuous movement of the pre-catalytic spliceosome, mode 1 2, frame 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Continuous movement of the pre-catalytic spliceosome, mode 1...

Fileemd_24096_additional_5.map
AnnotationContinuous movement of the pre-catalytic spliceosome, mode 1 2, frame 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pre-catalytic spliceosome

EntireName: Pre-catalytic spliceosome
Components
  • Complex: Pre-catalytic spliceosome

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Supramolecule #1: Pre-catalytic spliceosome

SupramoleculeName: Pre-catalytic spliceosome / type: complex / ID: 1 / Parent: 0
Details: Re-processing of the dataset EMPIAR-10180 to resolve the continuous movement of the system. Five frames of the first motion mode are attached as additional map files.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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
DetailsRe-processing of EMPIAR-10180.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3683

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: EMAN (ver. 2.91)
Details: Each 3D frame of the continuous movement movie includes 4000 particles. The maps are filtered to 20A for visualization.
Number images used: 4000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.91)
Final 3D classificationSoftware - Name: EMAN (ver. 2.91) / Details: Deep learning based manifold embedding

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