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- EMDB-11570: Human C Complex Spliceosome - MultiBody refined EXTENDED CORE -

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Basic information

Entry
Database: EMDB / ID: EMD-11570
TitleHuman C Complex Spliceosome - MultiBody refined EXTENDED CORE
Map data
Sample
  • Complex: Human C complex Spliceosome - High resolution core
Function / homology
Function and homology information


regulation of DNA double-strand break processing / striated muscle dense body / exon-exon junction subcomplex mago-y14 / post-spliceosomal complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / snRNP binding ...regulation of DNA double-strand break processing / striated muscle dense body / exon-exon junction subcomplex mago-y14 / post-spliceosomal complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / histone pre-mRNA DCP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNP / 3'-5' RNA helicase activity / regulation of translation at postsynapse, modulating synaptic transmission / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / negative regulation of excitatory postsynaptic potential / regulation of vitamin D receptor signaling pathway / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / Deadenylation of mRNA / embryonic brain development / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / pre-mRNA binding / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / Prp19 complex / poly(A) binding / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / M-decay: degradation of maternal mRNAs by maternally stored factors / P granule / RNA stem-loop binding / SMN-Sm protein complex / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / embryonic cranial skeleton morphogenesis / telomerase holoenzyme complex / positive regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / positive regulation by host of viral transcription / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / U2 snRNP / Notch binding / nuclear vitamin D receptor binding / RNA Polymerase II Transcription Termination / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U1 snRNP / RUNX3 regulates NOTCH signaling / muscle organ development / U2-type prespliceosome / NOTCH4 Intracellular Domain Regulates Transcription / K63-linked polyubiquitin modification-dependent protein binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ubiquitin-ubiquitin ligase activity / exploration behavior / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / lipid biosynthetic process / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / nuclear androgen receptor binding / cyclosporin A binding / spliceosomal complex assembly / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / Formation of paraxial mesoderm / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / protein K63-linked ubiquitination / mitotic G2 DNA damage checkpoint signaling / negative regulation of DNA damage response, signal transduction by p53 class mediator / mRNA 3'-splice site recognition / associative learning / blastocyst development
Similarity search - Function
Protein FRG1 / FRG1-like domain / Saf4/Yju2 protein / Splicing factor Yju2 / Saf4/Yju2 protein / Actin-crosslinking / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily ...Protein FRG1 / FRG1-like domain / Saf4/Yju2 protein / Splicing factor Yju2 / Saf4/Yju2 protein / Actin-crosslinking / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / : / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / mRNA splicing factor SYF2 / SYF2 splicing factor / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Helix hairpin bin domain superfamily / mRNA splicing factor Cwf21 domain / cwf21 domain / Pre-mRNA-processing factor 17 / : / STL11, N-terminal / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / : / U-box domain / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / : / : / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Myb-like DNA-binding domain / HAT (Half-A-TPR) repeat / Small ribonucleoprotein associated, SmB/SmN / Pre-mRNA-splicing factor Cwc2/Slt11 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / pre-mRNA splicing factor component / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / Small nuclear ribonucleoprotein D1 / MIF4G domain / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / U-box domain profile. / Leucine-rich repeat / Modified RING finger domain / Pre-mRNA-splicing factor Syf1-like / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / U-box domain / Sec63 Brl domain / Zinc finger, CCCH-type superfamily / : / Helicase associated domain (HA2), ratchet-like / zinc finger / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / Small nuclear ribonucleoprotein Sm D3 / Sec63 domain / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / Myb-type HTH DNA-binding domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
RNA helicase aquarius / Pre-mRNA-processing factor 17 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / Pre-mRNA-splicing factor SYF2 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein-associated proteins B and B' / Eukaryotic initiation factor 4A-III / Protein mago nashi homolog ...RNA helicase aquarius / Pre-mRNA-processing factor 17 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / Pre-mRNA-splicing factor SYF2 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein-associated proteins B and B' / Eukaryotic initiation factor 4A-III / Protein mago nashi 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 / SNW domain-containing protein 1 / Protein FRG1 / Pre-mRNA-processing-splicing factor 8 / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / Peptidylprolyl isomerase domain and WD repeat-containing protein 1 / Cell division cycle 5-like protein / Splicing factor YJU2 / Crooked neck-like protein 1 / Pre-mRNA-splicing factor CWC22 homolog / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / WD repeat-containing protein 70 / 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 protein 8A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBertram K
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SFB 860 Germany
CitationJournal: Mol Cell / Year: 2020
Title: Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome.
Authors: Karl Bertram / Leyla El Ayoubi / Olexandr Dybkov / Dmitry E Agafonov / Cindy L Will / Klaus Hartmuth / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann /
Abstract: Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core ...Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core resolution and 4.5-5.7 Å at its periphery, and aided by protein crosslinking we determine its molecular architecture. Our structure provides additional insights into the spliceosome's architecture between the catalytic steps of splicing, and how proteins aid formation of the spliceosome's catalytically active RNP (ribonucleoprotein) conformation. It reveals the spatial organization of the metazoan-specific proteins PPWD1, WDR70, FRG1, and CIR1 in human C complexes, indicating they stabilize functionally important protein domains and RNA structures rearranged/repositioned during the B to C transition. Structural comparisons with human B, C, and P complexes reveal an intricate cascade of RNP rearrangements during splicing catalysis, with intermediate RNP conformations not found in yeast, and additionally elucidate the structural basis for the sequential recruitment of metazoan-specific spliceosomal proteins.
History
DepositionAug 2, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7a5p
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7a5p
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11570.png

Downloads & links

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Map

FileDownload / File: emd_11570.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.032876723 - 0.10931318
Average (Standard dev.)-0.0007539676 (±0.004300183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 466.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z466.400466.400466.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ161186271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0330.109-0.001

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Supplemental data

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Sample components

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Entire : Human C complex Spliceosome - High resolution core

EntireName: Human C complex Spliceosome - High resolution core
Components
  • Complex: Human C complex Spliceosome - High resolution core

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Supramolecule #1: Human C complex Spliceosome - High resolution core

SupramoleculeName: Human C complex Spliceosome - High resolution core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#26
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa S3

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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

Concentration0.1 mg/mL
BufferpH: 7.9
Component:
ConcentrationFormulaName
20.0 mMHEPES-KOHHEPES-KOH, pH 7.9
1.5 mMMgCl2Magnesium Chloride
150.0 mMNaClSodium chlorideSodium chloride
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II
DetailsMonodisperse particle distribution

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -0.003 µm / Nominal defocus min: -0.001 µm / Nominal magnification: 132000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 28279 / Average exposure time: 1.0 sec. / Average electron dose: 120.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1751359
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69000

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