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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
SampleHuman C complex Spliceosome - High resolution core
Function / homology
Function and homology information


striated muscle dense body / regulation of histone H2B conserved C-terminal lysine ubiquitination / regulation of DNA double-strand break processing / negative regulation of selenocysteine insertion sequence binding / negative regulation of selenocysteine incorporation / cellular response to selenite ion / positive regulation of vitamin D receptor signaling pathway / post-spliceosomal complex / cellular response to wortmannin / cellular response to interleukin-2 ...striated muscle dense body / regulation of histone H2B conserved C-terminal lysine ubiquitination / regulation of DNA double-strand break processing / negative regulation of selenocysteine insertion sequence binding / negative regulation of selenocysteine incorporation / cellular response to selenite ion / positive regulation of vitamin D receptor signaling pathway / post-spliceosomal complex / cellular response to wortmannin / cellular response to interleukin-2 / cellular response to prolactin / exon-exon junction complex / U2 snRNP binding / snRNP binding / U7 snRNA binding / leucine zipper domain binding / histone pre-mRNA DCP binding / signal transduction involved in DNA damage checkpoint / regulation of translation at postsynapse, modulating synaptic transmission / transcription corepressor binding / U7 snRNP / histone pre-mRNA 3'end processing complex / negative regulation of excitatory postsynaptic potential / cis assembly of pre-catalytic spliceosome / methylosome / regulation of vitamin D receptor signaling pathway / histone mRNA metabolic process / exploration behavior / mitotic G2 DNA damage checkpoint / post-mRNA release spliceosomal complex / inner cell mass cell proliferation / RNA splicing, via transesterification reactions / generation of catalytic spliceosome for first transesterification step / RNA stem-loop binding / hair cycle / selenocysteine insertion sequence binding / positive regulation of astrocyte differentiation / positive regulation of neurogenesis / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / telomerase holoenzyme complex / U1 snRNP binding / protein phosphatase 1 binding / U2-type catalytic step 1 spliceosome / WD40-repeat domain binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / regulation of retinoic acid receptor signaling pathway / ubiquitin-ubiquitin ligase activity / P granule / C2H2 zinc finger domain binding / pICln-Sm protein complex / retinoic acid receptor binding / U4 snRNP / poly(A) binding / telomerase RNA binding / import into nucleus / pre-mRNA binding / small nuclear ribonucleoprotein complex / spliceosomal tri-snRNP complex / protein methylation / SMN-Sm protein complex / positive regulation by host of viral transcription / embryonic cranial skeleton morphogenesis / regulation of mRNA splicing, via spliceosome / Prp19 complex / vitamin D receptor binding / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / Notch binding / K63-linked polyubiquitin modification-dependent protein binding / U2 snRNP / commitment complex / U12-type spliceosomal complex / mRNA 3'-end processing / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / blastocyst development / cellular response to fibroblast growth factor stimulus / cellular response to brain-derived neurotrophic factor stimulus / muscle organ development / spliceosomal snRNP assembly / U2-type prespliceosome / small nucleolar ribonucleoprotein complex / positive regulation of transcription of Notch receptor target / U1 snRNP / mRNA 3'-splice site recognition / precatalytic spliceosome / translation regulator activity / lipid biosynthetic process / protein K63-linked ubiquitination / RNA export from nucleus / cyclosporin A binding / spliceosomal tri-snRNP complex assembly / retinoic acid receptor signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / U5 snRNP / U5 snRNA binding / U2 snRNA binding / positive regulation of histone H3-K4 methylation / regulation of alternative mRNA splicing, via spliceosome
RNA-binding motif protein 8 / CWF11 family / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / Tetratricopeptide repeat / WD40 repeat, conserved site / Pre-mRNA-splicing factor Isy1 / G-protein beta WD-40 repeat / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Homeobox-like domain superfamily ...RNA-binding motif protein 8 / CWF11 family / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / Tetratricopeptide repeat / WD40 repeat, conserved site / Pre-mRNA-splicing factor Isy1 / G-protein beta WD-40 repeat / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Homeobox-like domain superfamily / Pre-mRNA splicing factor component Cdc5p/Cef1 / PRP8 domain IV core / Spt5 C-terminal domain / Small nuclear ribonucleoprotein E / WD40-repeat-containing domain / Actin-crosslinking / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein Sm D2 / P-loop containing nucleoside triphosphate hydrolase / Pre-mRNA-processing-splicing factor 8 / Cyclophilin-like domain superfamily / Helix hairpin bin domain superfamily / Intron-binding protein aquarius, N-terminal / Leucine-rich repeat domain superfamily / Pre-mRNA-processing factor 17 / RBM8, RNA recognition motif / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Myb domain / Small nuclear ribonucleoprotein Sm D3 / Pre-mRNA-splicing factor 19 / Tetratricopeptide-like helical domain superfamily / PRO8NT domain / PROCN domain / Nucleotide-binding alpha-beta plait domain superfamily / PROCT domain / Tetratricopeptide repeat-containing domain / Domain of unknown function DUF1605 / DEAD/DEAH box helicase domain / Zinc finger, RING/FYVE/PHD-type / mRNA splicing factor Cwf21 domain / mRNA splicing factor SYF2 / Helicase superfamily 1/2, ATP-binding domain / SKI-interacting protein, SKIP / RNA helicase, DEAD-box type, Q motif / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / MIF4G-like domain superfamily / Pre-mRNA-splicing factor SPF27 / Armadillo-type fold / LSM domain superfamily / Peptidyl-prolyl cis-trans isomerase E / Protein FRG1 / Sm-like protein Lsm6/SmF / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein G / Ribonuclease H-like superfamily / RNA recognition motif domain / Small nuclear ribonucleoprotein F / Initiation factor eIF-4 gamma, MA3 / MIF4G-like, type 3 / Helicase, C-terminal / U box domain / U2A'/phosphoprotein 32 family A, C-terminal / DNA2/NAM7 helicase-like, C-terminal / HAT (Half-A-TPR) repeat / WD40-repeat-containing domain superfamily / Winged helix DNA-binding domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Mago nashi superfamily / Zinc finger, CCCH-type superfamily / Pre-mRNA-splicing factor Isy1 superfamily / MPN domain / DNA2/NAM7 helicase, helicase domain / Brr2, N-terminal helicase PWI domain / WD40 repeat / Pre-mRNA-processing factor 19 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Leucine-rich repeat / RNA-binding domain superfamily / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / SKI-interacting protein SKIP, SNW domain / JAB1/MPN/MOV34 metalloenzyme domain / Small nuclear ribonucleoprotein D1 / Zinc finger, CCCH-type / Saf4/Yju2 protein / ATP-dependent RNA helicase DEAD-box, conserved site / Ricin B, lectin domain / Prp8 RNase domain IV, fingers region / SANT/Myb domain / LSM domain, eukaryotic/archaea-type / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Helicase-associated domain / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / Prp8 RNase domain IV, palm region / Sec63 domain / C2 domain superfamily / Mago nashi protein / Pre-mRNA-splicing factor Cwc2/Slt11
RNA helicase aquarius / Protein FRG1 / Serine/arginine repetitive matrix protein 2 / Peptidyl-prolyl cis-trans isomerase E / Pre-mRNA-processing factor 19 / Pre-mRNA-splicing factor ISY1 homolog / WD repeat-containing protein 70 / Pre-mRNA-splicing factor RBM22 / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor CWC22 homolog ...RNA helicase aquarius / Protein FRG1 / Serine/arginine repetitive matrix protein 2 / Peptidyl-prolyl cis-trans isomerase E / Pre-mRNA-processing factor 19 / Pre-mRNA-splicing factor ISY1 homolog / WD repeat-containing protein 70 / Pre-mRNA-splicing factor RBM22 / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor CWC22 homolog / Crooked neck-like protein 1 / Splicing factor YJU2 / Cell division cycle 5-like protein / Peptidylprolyl isomerase domain and WD repeat-containing protein 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / Pre-mRNA-processing-splicing factor 8 / SNW domain-containing protein 1 / Pre-mRNA-processing factor 17 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein E / Protein mago nashi homolog / Eukaryotic initiation factor 4A-III / Small nuclear ribonucleoprotein-associated proteins B and B' / U2 small nuclear ribonucleoprotein A' / U2 small nuclear ribonucleoprotein B'' / Pre-mRNA-splicing factor SYF2 / Pre-mRNA-splicing factor SPF27 / U5 small nuclear ribonucleoprotein 200 kDa helicase / RNA-binding protein 8A
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.
Validation ReportPDB-ID: 7a5p

SummaryFull reportAbout validation report
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

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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 440 pix.
= 466.4 Å
1.06 Å/pix.
x 440 pix.
= 466.4 Å
1.06 Å/pix.
x 440 pix.
= 466.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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 / Number of components: 1

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Component #1: protein, Human C complex Spliceosome - High resolution core

ProteinName: Human C complex Spliceosome - High resolution core / Recombinant expression: No
SourceSpecies: Homo sapiens (human) / Strain: HeLa S3

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/mL / pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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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: 120 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 132000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1.0 - -3.0 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: 28279

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 69000
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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