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- EMDB-4240: Human Bact spliceosome state 8 unmasked -

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Entry
Database: EMDB / ID: EMD-4240
TitleHuman Bact spliceosome state 8 unmasked
Map data
Samplehuman Bact spliceosome state 1 unmasked
Function / homology
Function and homology information


isopeptide cross-linking via N6-glycyl-L-lysine / post-spliceosomal complex / RES complex / U2-type prespliceosome assembly / positive regulation of vitamin D receptor signaling pathway / snoRNA splicing / cellular response to interleukin-2 / cellular response to wortmannin / U11/U12 snRNP / cellular response to prolactin ...isopeptide cross-linking via N6-glycyl-L-lysine / post-spliceosomal complex / RES complex / U2-type prespliceosome assembly / positive regulation of vitamin D receptor signaling pathway / snoRNA splicing / cellular response to interleukin-2 / cellular response to wortmannin / U11/U12 snRNP / cellular response to prolactin / negative regulation of chemokine-mediated signaling pathway / snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / leucine zipper domain binding / U7 snRNP / signal transduction involved in DNA damage checkpoint / transcription corepressor binding / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / regulation of retinoic acid receptor signaling pathway / methylosome / post-mRNA release spliceosomal complex / histone mRNA metabolic process / blastocyst formation / generation of catalytic spliceosome for first transesterification step / regulation of vitamin D receptor signaling pathway / inner cell mass cell proliferation / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / positive regulation of androgen receptor activity / production of miRNAs involved in gene silencing by miRNA / hair cycle / positive regulation of astrocyte differentiation / U2-type catalytic step 1 spliceosome / telomerase holoenzyme complex / pICln-Sm protein complex / U1 snRNP binding / protein phosphatase 1 binding / U4 snRNP / U2-type precatalytic spliceosome / WD40-repeat domain binding / positive regulation of neurogenesis / positive regulation of mRNA splicing, via spliceosome / ubiquitin-ubiquitin ligase activity / P granule / retinoic acid receptor binding / C2H2 zinc finger domain binding / small nuclear ribonucleoprotein complex / spliceosomal tri-snRNP complex / telomerase RNA binding / positive regulation by host of viral transcription / SMN-Sm protein complex / import into nucleus / pre-mRNA binding / regulation of mRNA splicing, via spliceosome / protein methylation / commitment complex / U2 snRNP / U2-type catalytic step 2 spliceosome / mRNA cis splicing, via spliceosome / Prp19 complex / Notch binding / U12-type spliceosomal complex / vitamin D receptor binding / poly(A) binding / K63-linked polyubiquitin modification-dependent protein binding / Cul4-RING E3 ubiquitin ligase complex / positive regulation of gene expression, epigenetic / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / U2-type prespliceosome / spliceosomal snRNP assembly / sno(s)RNA-containing ribonucleoprotein complex / mRNA 3'-end processing / U1 snRNP / positive regulation of transcription of Notch receptor target / mRNA 3'-splice site recognition / precatalytic spliceosome / lipid biosynthetic process / blastocyst development / protein K63-linked ubiquitination / androgen receptor binding / RNA export from nucleus / spliceosomal tri-snRNP complex assembly / cyclosporin A binding / cellular response to fibroblast growth factor stimulus / U5 snRNP / U5 snRNA binding / positive regulation of transforming growth factor beta receptor signaling pathway / U2 snRNA binding / positive regulation of histone H3-K4 methylation / protein localization to nucleus / U6 snRNA binding / pre-mRNA intronic binding / termination of RNA polymerase II transcription / RNA processing
WD40/YVTN repeat-like-containing domain superfamily / Zinc finger, CCCH-type / Splicing factor 3B, subunit 5 / Sm-like protein Lsm6/SmF / Peptidyl-prolyl cis-trans isomerase E / Armadillo-type fold / SWAP/Surp / Forkhead-associated (FHA) domain / RNA recognition motif domain / JAB1/MPN/MOV34 metalloenzyme domain ...WD40/YVTN repeat-like-containing domain superfamily / Zinc finger, CCCH-type / Splicing factor 3B, subunit 5 / Sm-like protein Lsm6/SmF / Peptidyl-prolyl cis-trans isomerase E / Armadillo-type fold / SWAP/Surp / Forkhead-associated (FHA) domain / RNA recognition motif domain / JAB1/MPN/MOV34 metalloenzyme domain / Ubiquitin-like domain / SKI-interacting protein, SKIP / Elongation factor EFG, domain V-like / Matrin/U1-C, C2H2-type zinc finger / Ricin B, lectin domain / Translational (tr)-type GTP-binding domain / SANT/Myb domain / LSM domain, eukaryotic/archaea-type / Leucine-rich repeat / Helicase, C-terminal / WD40 repeat / Small ribonucleoprotein associated, SmB/SmN / Zinc finger, RING-type, conserved site / Zinc finger, RING-type / Ribosomal protein S5 domain 2-type fold / CWF11 family / Spt5 C-terminal domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Splicing factor SF3a60 subunit C-terminal / Splicing factor 3A subunit 1 / PRP8 domain IV core / Splicing factor SF3a60 binding domain / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / MIF4G-like domain superfamily / Myb domain / WD40 repeat, conserved site / Tetratricopeptide repeat / RNA recognition motif, spliceosomal PrP8 / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Bud13 / BUD31/G10-related, conserved site / WD40-repeat-containing domain / G10 protein / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / PROCN domain / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / LSM domain superfamily / DEAD/DEAH box helicase domain / Domain of unknown function DUF1605 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Ribonuclease H-like superfamily / PRO8NT domain / Nucleotide-binding alpha-beta plait domain superfamily / Homeobox-like domain superfamily / PROCT domain / Tetratricopeptide repeat-containing domain / Zinc finger, RING/FYVE/PHD-type / mRNA splicing factor Cwf21 domain / Pre-mRNA-splicing factor 19 / Helicase superfamily 1/2, ATP-binding domain / Ribosomal protein S5 domain 2-type fold, subgroup / Immunoglobulin E-set / Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor Isy1 / Translation protein, beta-barrel domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Translation elongation factor EFTu-like, domain 2 / PWI domain / SAP domain / HAT (Half-A-TPR) repeat / U2A'/phosphoprotein 32 family A, C-terminal / Matrin/U1-C-like, C2H2-type zinc finger / U box domain / MIF4G-like, type 3 / Initiation factor eIF-4 gamma, MA3 / SKI-interacting protein SKIP, SNW domain / Sec63 domain / SMAD/FHA domain superfamily / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Small GTP-binding protein domain / PHF5-like / Translation elongation factor EFG/EF2, domain IV / PSP, proline-rich / Pre-mRNA-splicing factor Cwf15/Cwc15 / Domain of unknown function DUF382 / Helicase-associated domain / Pre-mRNA-splicing factor SPF27 / Small nuclear ribonucleoprotein E / G-protein beta WD-40 repeat / Small nuclear ribonucleoprotein Sm D2 / WD40-repeat-containing domain superfamily / Pre-mRNA-splicing factor CWC24-like / SF3A3 domain / Pre-mRNA-splicing factor Cwc2/Slt11 / Pre-mRNA-processing factor 19
Splicing factor 3B subunit 6 / BUD13 homolog / Splicing factor 3A subunit 1 / Pre-mRNA-processing-splicing factor 8 / Spliceosome-associated protein CWC27 homolog / PHD finger-like domain-containing protein 5A / Serine/arginine repetitive matrix protein 1 / Smad nuclear-interacting protein 1 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein ...Splicing factor 3B subunit 6 / BUD13 homolog / Splicing factor 3A subunit 1 / Pre-mRNA-processing-splicing factor 8 / Spliceosome-associated protein CWC27 homolog / PHD finger-like domain-containing protein 5A / Serine/arginine repetitive matrix protein 1 / Smad nuclear-interacting protein 1 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / Splicing factor 3B subunit 5 / RNA-binding motif protein, X-linked 2 / Crooked neck-like protein 1 / Splicing factor 3A subunit 2 / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-splicing factor ISY1 homolog / Pre-mRNA-processing factor 19 / Peptidyl-prolyl cis-trans isomerase E / Serine/arginine repetitive matrix protein 2 / Pre-mRNA-splicing factor CWC22 homolog / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3B subunit 3 / U2 small nuclear ribonucleoprotein A' / E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / RNA helicase aquarius / Pre-mRNA-processing factor 17 / Splicing factor 3B subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / U2 small nuclear ribonucleoprotein B'' / Small nuclear ribonucleoprotein-associated proteins B and B' / SNW domain-containing protein 1 / Protein BUD31 homolog / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Splicing factor 3A subunit 3 / Splicing factor 3B subunit 2 / Peptidyl-prolyl cis-trans isomerase-like 1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsHaselbach D / Komarov I / Agafonov D / Kastner B / Luehrmann R / Stark H
CitationJournal: Cell / Year: 2018
Title: Structure and Conformational Dynamics of the Human Spliceosomal B Complex.
Authors: David Haselbach / Ilya Komarov / Dmitry E Agafonov / Klaus Hartmuth / Benjamin Graf / Olexandr Dybkov / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark /
Abstract: The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In ...The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In the B state, the spliceosome is activated but not catalytically primed, so that it is functionally blocked prior to the first catalytic step of splicing. The spliceosomal core is similar to the yeast B spliceosome; important differences include the presence of the RNA helicase aquarius and peptidyl prolyl isomerases. To examine the overall dynamic behavior of the purified spliceosome, we developed a principal component analysis-based approach. Calculating the energy landscape revealed eight major conformational states, which we refined to higher resolution. Conformational differences of the highly flexible structural components between these eight states reveal how spliceosomal components contribute to the assembly of the spliceosome, allowing it to generate a dynamic interaction network required for its subsequent catalytic activation.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 22, 2017-
Header (metadata) releaseFeb 7, 2018-
Map releaseFeb 7, 2018-
UpdateFeb 7, 2018-
Current statusFeb 7, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ff7
  • Surface level: 0.013
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4240.png

Downloads & links

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Map

FileDownload / File: emd_4240.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 420 pix.
= 487.2 Å		1.16 Å/pix.
x 420 pix.
= 487.2 Å		1.16 Å/pix.
x 420 pix.
= 487.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.014408626 - 0.06181489
Average (Standard dev.)0.00064544595 (±0.004007307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 487.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z487.200487.200487.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.0140.0620.001

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Supplemental data

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Sample components

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Entire human Bact spliceosome state 1 unmasked

EntireName: human Bact spliceosome state 1 unmasked / Number of components: 1

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Component #1: protein, human Bact spliceosome state 1 unmasked

ProteinName: human Bact spliceosome state 1 unmasked / Recombinant expression: No
MassTheoretical: 4.5 MDa
SourceSpecies: Homo sapiens (human) / Strain: HELA

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.05 mg/mL / pH: 7.9
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 75 % / Details: blot with blotting sensor.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 59000.0 X (nominal) / Cs: 0.001 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 4500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 32000 / Sampling size: 14 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 165853
3D reconstructionSoftware: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

6ff7

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