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

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Basic information

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


RES complex / post-spliceosomal complex / negative regulation of chemokine-mediated signaling pathway / regulation of vitamin D receptor signaling pathway / oocyte development / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / blastocyst development / post-mRNA release spliceosomal complex / U2 snRNP binding ...RES complex / post-spliceosomal complex / negative regulation of chemokine-mediated signaling pathway / regulation of vitamin D receptor signaling pathway / oocyte development / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / blastocyst development / post-mRNA release spliceosomal complex / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / blastocyst formation / 3'-5' RNA helicase activity / cis assembly of pre-catalytic spliceosome / histone pre-mRNA 3'end processing complex / nuclear histone mRNA catabolic process / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / inner cell mass cell proliferation / miRNA processing / alternative mRNA splicing, via spliceosome / poly(A) binding / 7-methylguanosine cap hypermethylation / U12-type spliceosomal complex / nuclear retinoic acid receptor binding / embryonic brain development / positive regulation of mRNA splicing, via spliceosome / U1 snRNP binding / C2H2 zinc finger domain binding / pICln-Sm protein complex / regulation of mRNA splicing, via spliceosome / U2-type catalytic step 1 spliceosome / methylosome / RNA splicing, via transesterification reactions / mRNA 3'-end processing / sno(s)RNA-containing ribonucleoprotein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / protein methylation / splicing factor binding / spliceosomal tri-snRNP complex / positive regulation of vitamin D receptor signaling pathway / P granule / commitment complex / U4 snRNP / snRNP binding / host-mediated activation of viral transcription / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Notch binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U2-type spliceosomal complex / nuclear vitamin D receptor binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / NOTCH4 Intracellular Domain Regulates Transcription / telomerase holoenzyme complex / telomerase RNA binding / pre-mRNA binding / positive regulation of neurogenesis / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U1 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH3 Intracellular Domain Regulates Transcription / mRNA stabilization / U2-type prespliceosome / RHOBTB1 GTPase cycle / K63-linked polyubiquitin modification-dependent protein binding / protein peptidyl-prolyl isomerization / nuclear androgen receptor binding / cyclosporin A binding / generation of catalytic spliceosome for second transesterification step / precatalytic spliceosome / ubiquitin-ubiquitin ligase activity / Notch-HLH transcription pathway / Formation of paraxial mesoderm / lipid biosynthetic process / pattern recognition receptor activity / WD40-repeat domain binding / positive regulation of transforming growth factor beta receptor signaling pathway / mRNA 3'-splice site recognition / regulation of RNA splicing / SMAD binding / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / positive regulation of transcription by RNA polymerase III / spliceosomal complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Prp19 complex / negative regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex assembly / U5 snRNP / U5 snRNA binding / ovarian follicle development
Similarity search - Function
: / : / Pre-mRNA-splicing factor CWC24-like / Ist3-like, RNA recognition motif / : / Bud13 / : / Pre-mRNA-splicing factor of RES complex / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily ...: / : / Pre-mRNA-splicing factor CWC24-like / Ist3-like, RNA recognition motif / : / Bud13 / : / Pre-mRNA-splicing factor of RES complex / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / : / Prp19 WD40 domain / : / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / : / RBM22 CCCH zinc finger domain / PWI domain superfamily / PWI domain / PWI domain profile. / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / SF3B6, RNA recognition motif / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / Helix hairpin bin domain superfamily / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / PWI domain / PWI, domain in splicing factors / : / : / Cactus-binding C-terminus of cactin protein / Splicing factor 3A subunit 1, ubiquitin domain / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / : / Replication stress response SDE2 C-terminal / mRNA splicing factor Cwf21 domain / cwf21 domain / SF3A2 domain / : / 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 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA-processing factor 17 / Splicing factor 3A subunit 1 / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Pre-mRNA splicing factor PRP21 like protein / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / : / Prp19/Pso4-like / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / G10 protein signature 2. / : / : / 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 / BUD31/G10-related, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / G10 protein signature 1. / Splicing factor 3B, subunit 5 / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / : / STL11, N-terminal / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / DNA2/NAM7 helicase, helicase domain / Zinc-finger of C2H2 type / AAA domain / U-box domain / SKI-interacting protein SKIP, SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / SKI-interacting protein, SKIP / SKIP/SNW domain / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / PSP, proline-rich / Pre-mRNA-splicing factor Cwc2/Slt11 / PSP / proline-rich domain in spliceosome associated proteins / : / Initiation factor eIF-4 gamma, MA3
Similarity search - Domain/homology
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'' / 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'' / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein-associated proteins B and B' / 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 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3B subunit 3 / Splicing factor 3A subunit 2 / 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 / BUD13 homolog / Splicing factor 3B subunit 5 / Crooked neck-like protein 1 / Pre-mRNA-splicing factor CWC22 homolog / 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 / RNA-binding motif protein, X-linked 2 / Splicing factor 3B subunit 6 / Peptidyl-prolyl cis-trans isomerase-like 1
Similarity search - Component
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.
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
  • Imaged by UCSF Chimera
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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
Components
  • Complex: human Bact spliceosome state 1 unmasked

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Supramolecule #1: human Bact spliceosome state 1 unmasked

SupramoleculeName: human Bact spliceosome state 1 unmasked / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: HELA
Molecular weightTheoretical: 4.5 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

Concentration0.05 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMNaCl
1.5 mMMgCl2
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: blot with blotting sensor.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureComa free - Residual tilt: 14.0 mrad
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector with two hexapoles elements
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 32000 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3300000
CTF correctionSoftware - Name: Gctf
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 165853
Initial angle assignmentType: OTHER / Software - Name: EMAN2
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationNumber classes: 220 / Software - Name: RELION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6ff7:
human Bact spliceosome core structure

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