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- EMDB-4525: Human post-catalytic spliceosome (P complex) stalled with DHX8 K5... -

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Basic information

Entry
Database: EMDB / ID: EMD-4525
TitleHuman post-catalytic spliceosome (P complex) stalled with DHX8 K594A mutant, overall map
Map data
SampleHuman post-catalytic P complex spliceosome
  • (ATP-dependent RNA helicase ...) x 2
  • MINX introns and exons
  • (nucleic-acidNucleic acid) x 5
  • Eukaryotic initiation factor 4A-III
  • RNA-binding protein 8A
  • Protein mago nashi homolog 2
  • Pre-mRNA-processing-splicing factor 8
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • PRKR-interacting protein 1
  • Cactin
  • Protein FAM32A
  • (Pre-mRNA-splicing factor ...) x 6
  • Pleiotropic regulator 1
  • SNW domain-containing protein 1
  • Protein BUD31 homolog
  • Cell division cycle 5-like protein
  • Spliceosome-associated protein CWC15 homolog
  • Serine/arginine repetitive matrix protein 2
  • Crooked neck-like protein 1
  • Intron-binding protein aquarius
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • NF-kappa-B-activating protein
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • Peptidyl-prolyl cis-trans isomerase-like 1
  • (Pre-mRNA-processing factor ...) x 2
  • Replication stress response regulator SDE2
  • (ligand) x 6
Function / homology
Function and homology information


Dual incision in TC-NER / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / Regulation of expression of SLITs and ROBOs / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / RUNX3 regulates NOTCH signaling / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / RNA Polymerase II Transcription Termination / mRNA 3'-end processing ...Dual incision in TC-NER / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / Regulation of expression of SLITs and ROBOs / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / RUNX3 regulates NOTCH signaling / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / RNA Polymerase II Transcription Termination / mRNA 3'-end processing / mRNA Splicing - Minor Pathway / mRNA Splicing - Major Pathway / Gap-filling DNA repair synthesis and ligation in TC-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Deadenylation of mRNA / Notch-HLH transcription pathway / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Constitutive Signaling by NOTCH1 PEST Domain Mutants / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / NOTCH1 Intracellular Domain Regulates Transcription / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / snRNP Assembly / Pre-NOTCH Transcription and Translation / Transport of Mature mRNA derived from an Intron-Containing Transcript / ISG15 antiviral mechanism / SLBP independent Processing of Histone Pre-mRNAs / negative regulation of selenocysteine insertion sequence binding / negative regulation of selenocysteine incorporation / positive regulation of vitamin D receptor signaling pathway / cellular response to selenite ion / granulocyte differentiation / cellular response to wortmannin / cellular response to interleukin-2 / negative regulation of interleukin-8 production / cellular response to prolactin / spliceosomal complex disassembly / regulation of cell cycle arrest / U2 snRNP binding / snRNP binding / U7 snRNA binding / exon-exon junction complex / histone pre-mRNA DCP binding / leucine zipper domain binding / U7 snRNP / negative regulation of interferon-beta production / pre-mRNA 3'-splice site binding / signal transduction involved in DNA damage checkpoint / histone pre-mRNA 3'end processing complex / negative regulation of excitatory postsynaptic potential / hematopoietic stem cell proliferation / exploration behavior / selenocysteine insertion sequence binding / cis assembly of pre-catalytic spliceosome / methylosome / mitotic G2 DNA damage checkpoint / go:0034459: / regulation of translation at postsynapse, modulating synaptic transmission / inner cell mass cell proliferation / histone mRNA metabolic process / regulation of mRNA splicing, via spliceosome / regulation of vitamin D receptor signaling pathway / U2-type catalytic step 1 spliceosome / telomerase holoenzyme complex / renal system process / positive regulation of neurogenesis / negative regulation of toll-like receptor signaling pathway / RNA splicing, via transesterification reactions / generation of catalytic spliceosome for first transesterification step / hair cycle / protein phosphatase 1 binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein kinase inhibitor activity / negative regulation of phosphorylation / positive regulation of androgen receptor activity / RNA stem-loop binding / transcription corepressor binding / ubiquitin-ubiquitin ligase activity / mRNA 3'-splice site recognition / U2-type precatalytic spliceosome / U1 snRNP binding / WD40-repeat domain binding / alternative mRNA splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / positive regulation of astrocyte differentiation / pICln-Sm protein complex / telomerase RNA binding / import into nucleus / U4 snRNP / small nuclear ribonucleoprotein complex / regulation of retinoic acid receptor signaling pathway / second spliceosomal transesterification activity / U5 snRNA binding / negative regulation of lipopolysaccharide-mediated signaling pathway / C2H2 zinc finger domain binding / post-mRNA release spliceosomal complex / retinoic acid receptor binding / SMN-Sm protein complex / Notch binding / U2 snRNA binding
RNA recognition motif domain / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Pre-mRNA-splicing factor SPF27 / RNA-binding motif protein 8 / Helicase-associated domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / Translation elongation factor EFG/EF2, domain IV / Sec63 domain / NF-kappa-B-activating protein, C-terminal ...RNA recognition motif domain / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Pre-mRNA-splicing factor SPF27 / RNA-binding motif protein 8 / Helicase-associated domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / Translation elongation factor EFG/EF2, domain IV / Sec63 domain / NF-kappa-B-activating protein, C-terminal / Translation elongation factor EFTu-like, domain 2 / Mago nashi protein / SKI-interacting protein SKIP, SNW domain / Initiation factor eIF-4 gamma, MA3 / MIF4G-like, type 3 / U box domain / Homeobox-like domain superfamily / PRKR-interacting protein 1 / HAT (Half-A-TPR) repeat / Nucleotide-binding alpha-beta plait domain superfamily / Protein FAM32A / mRNA splicing factor SYF2 / mRNA splicing factor Cwf21 domain / Zinc finger, RING/FYVE/PHD-type / Tetratricopeptide repeat-containing domain / PROCT domain / PROCN domain / LSM domain superfamily / PRO8NT domain / Nucleic acid-binding, OB-fold / Ribonuclease H-like superfamily / Tetratricopeptide-like helical domain superfamily / Domain of unknown function DUF1605 / DEAD/DEAH box helicase domain / U2A'/phosphoprotein 32 family A, C-terminal / S1 domain / Helicase superfamily 1/2, ATP-binding domain / NF-kappa-B-activating protein C-terminal domain / Elongation factor Tu domain 2 / Elongation factor G, domain IV / Helicase associated domain (HA2) / U-box domain / Cwf15/Cwc15 cell cycle control protein / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Protein of unknown function (DUF1168) / MA3 domain / Oligonucleotide/oligosaccharide-binding (OB)-fold / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / PROCT (NUC072) domain / SYF2 splicing factor / cwf21 domain / Sec63 Brl domain / Mago nashi protein / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / SANT/Myb domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / G10 protein / WD40 repeat / Helicase, C-terminal / Leucine-rich repeat / LSM domain, eukaryotic/archaea-type / Transcription factor, GTP-binding domain / SKIP/SNW domain / Ricin B, lectin domain / Elongation factor EFG, domain V-like / ATP-dependent RNA helicase DEAD-box, conserved site / Zinc finger, CCCH-type / JAB1/MPN/MOV34 metalloenzyme domain / LSM domain / HAT (Half-A-TPR) repeat / Pre-mRNA-splicing factor 19 / RNA helicase, DEAD-box type, Q motif / Prp19/Pso4-like / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / Winged helix DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / RNA-binding domain superfamily / C2 domain superfamily / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / EF-G domain III/V-like / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / Zinc finger, CCCH-type superfamily / Small nuclear ribonucleoprotein D1 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / RBM8, RNA recognition motif / Pre-mRNA-processing factor 17 / Mago nashi superfamily / MPN domain / Intron-binding protein aquarius, N-terminal / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Elongation factor G C-terminus / S1 RNA binding domain / WD domain, G-beta repeat / Helicase conserved C-terminal domain / DEAD/DEAH box helicase / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Elongation factor Tu GTP binding domain
Pleiotropic regulator 1 / PRKR-interacting protein 1 / Pre-mRNA-processing-splicing factor 8 / NF-kappa-B-activating protein / Cactin / Protein mago nashi homolog 2 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / Crooked neck-like protein 1 / Pre-mRNA-splicing factor CWC22 homolog ...Pleiotropic regulator 1 / PRKR-interacting protein 1 / Pre-mRNA-processing-splicing factor 8 / NF-kappa-B-activating protein / Cactin / Protein mago nashi homolog 2 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / Crooked neck-like protein 1 / Pre-mRNA-splicing factor CWC22 homolog / 116 kDa U5 small nuclear ribonucleoprotein component / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-processing factor 19 / Serine/arginine repetitive matrix protein 2 / Peptidyl-prolyl cis-trans isomerase-like 1 / Protein FAM32A / Replication stress response regulator SDE2 / ATP-dependent RNA helicase DHX8 / RNA helicase aquarius / Small nuclear ribonucleoprotein-associated proteins B and B' / Pre-mRNA-processing factor 17 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / Pre-mRNA-splicing factor SLU7 / Pre-mRNA-splicing factor SYF2 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' / Eukaryotic initiation factor 4A-III / 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 / RNA-binding protein 8A
Biological speciesHomo sapiens (human) / Human adenovirus 2 / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFica SM / Oubridge C / Wilkinson ME / Newman AJ / Nagai K
CitationJournal: Science / Year: 2019
Title: A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation.
Authors: Sebastian M Fica / Chris Oubridge / Max E Wilkinson / Andrew J Newman / Kiyoshi Nagai /
Abstract: During exon ligation, the spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a ...During exon ligation, the spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a conformation stabilized by Prp18 and Prp8. Here we present the 3.3-angstrom cryo-electron microscopy structure of a human postcatalytic spliceosome just after exon ligation. The 3'SS docks at the active site through conserved RNA interactions in the absence of Prp18. Unexpectedly, the metazoan-specific FAM32A directly bridges the 5'-exon and intron 3'SS of pre-mRNA and promotes exon ligation, as shown by functional assays. CACTIN, SDE2, and NKAP-factors implicated in alternative splicing-further stabilize the catalytic conformation of the spliceosome during exon ligation. Together these four proteins act as exon ligation factors. Our study reveals how the human spliceosome has co-opted additional proteins to modulate a conserved RNA-based mechanism for 3'SS selection and to potentially fine-tune alternative splicing at the exon ligation stage.
Validation ReportPDB-ID: 6qdv

SummaryFull reportAbout validation report
DateDeposition: Jan 3, 2019 / Header (metadata) release: Feb 20, 2019 / Map release: Feb 20, 2019 / Update: Feb 27, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6qdv
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4525.map.gz / Format: CCP4 / Size: 262.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 410 pix.
= 492. Å
1.2 Å/pix.
x 410 pix.
= 492. Å
1.2 Å/pix.
x 410 pix.
= 492. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.10098974 - 0.17720254
Average (Standard dev.)0.000077332166 (±0.0050888886)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions410410410
Spacing410410410
CellA=B=C: 492.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z410410410
origin x/y/z0.0000.0000.000
length x/y/z492.000492.000492.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS410410410
D min/max/mean-0.1010.1770.000

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Supplemental data

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Sample components

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Entire Human post-catalytic P complex spliceosome

EntireName: Human post-catalytic P complex spliceosome / Number of components: 54

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Component #1: protein, Human post-catalytic P complex spliceosome

ProteinName: Human post-catalytic P complex spliceosome / Recombinant expression: No
MassTheoretical: 3.0 MDa

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Component #2: protein, Human post-catalytic P complex spliceosome

ProteinName: Human post-catalytic P complex spliceosome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #3: protein, ATP-dependent RNA helicase DHX8

ProteinName: ATP-dependent RNA helicase DHX8 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #4: protein, MINX introns and exons

ProteinName: MINX introns and exons / Recombinant expression: No
SourceSpecies: Human adenovirus 2
Source (engineered)Expression System: synthetic construct (others)

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Component #5: nucleic-acid, U2 snRNA

nucleic acidName: U2 snRNAU2 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUCGCUUCUC GGCCUUUUGG CUAAGAUCAA GUGUAGUAUC UGUUCUUAUC AGUUUAAUAU CUGAUACGUC CUCUAUCCGA GGACAAUAUA UUAAAAGAUU UUUGGAACUC AGGGAGAUGG AAUAGGAGCU UGCUCCGUCC ACUCCACGCA UCGACCUGGU AUUGCAGUAC CUCCAGGAAC GGUGCACCC
MassTheoretical: 60.459621 kDa
SourceSpecies: Human (human)

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Component #6: nucleic-acid, U5 snRNA

nucleic acidName: U5 snRNAU5 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUACUCUGGU UUCUCUUCAG AUCGCAUAAA UCUUUCGCCU UUUACUAAAG AUUUCCGUGG AGAGGAACAA CUCUGAGUCU UAACCCAAUU UUUUGAGCCU UGCCUUGGCA AGGCUA
MassTheoretical: 36.908668 kDa
SourceSpecies: Human (human)

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Component #7: nucleic-acid, U6 snRNA

nucleic acidName: U6 snRNAU6 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUGCUCGCUU CGGCAGCACA UAUACUAAAA UUGGAACGAU ACAGAGAAGA UUAGCAUGGC CCCUGCGCAA GGAUGACACG CAAAUUCGUG AAGCGUUCCA UAUUUU
MassTheoretical: 34.09827 kDa
SourceSpecies: Human (human)

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Component #8: protein, Eukaryotic initiation factor 4A-III

ProteinName: Eukaryotic initiation factor 4A-III / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.691359 kDa
SourceSpecies: Human (human)

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Component #9: protein, RNA-binding protein 8A

ProteinName: RNA-binding protein 8A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.370526 kDa
SourceSpecies: Human (human)

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Component #10: protein, Protein mago nashi homolog 2

ProteinName: Protein mago nashi homolog 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.929314 kDa
SourceSpecies: Human (human)

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Component #11: protein, Pre-mRNA-processing-splicing factor 8

ProteinName: Pre-mRNA-processing-splicing factor 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 273.97425 kDa
SourceSpecies: Human (human)

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Component #12: protein, U5 small nuclear ribonucleoprotein 200 kDa helicase

ProteinName: U5 small nuclear ribonucleoprotein 200 kDa helicase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 197.053984 kDa
SourceSpecies: Human (human)

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Component #13: protein, 116 kDa U5 small nuclear ribonucleoprotein component

ProteinName: 116 kDa U5 small nuclear ribonucleoprotein component / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 101.231938 kDa
SourceSpecies: Human (human)

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Component #14: protein, PRKR-interacting protein 1

ProteinName: PRKR-interacting protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.476882 kDa
SourceSpecies: Human (human)

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Component #15: nucleic-acid, Ligated exons: MINX mRNA

nucleic acidName: Ligated exons: MINX mRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGCCUCCGAA CGCU
MassTheoretical: 4.4377 kDa
SourceSpecies: Human adenovirus 2

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Component #16: protein, Cactin

ProteinName: Cactin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.210249 kDa
SourceSpecies: Human (human)

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Component #17: protein, Protein FAM32A

ProteinName: Protein FAM32A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.269374 kDa
SourceSpecies: Human (human)

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Component #18: protein, Pre-mRNA-splicing factor CWC22 homolog

ProteinName: Pre-mRNA-splicing factor CWC22 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.646578 kDa
SourceSpecies: Human (human)

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Component #19: nucleic-acid, Intron lariat: MINX RNA

nucleic acidName: Intron lariat: MINX RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUAAGAGCCU AGCAUGUAGA ANNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN UGAUGAUGUC AUACUUAUCC UNNNNNNNNN CAG
MassTheoretical: 27.772039 kDa
SourceSpecies: Human adenovirus 2

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Component #20: protein, Pleiotropic regulator 1

ProteinName: Pleiotropic regulator 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.782395 kDa
SourceSpecies: Human (human)

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Component #21: protein, SNW domain-containing protein 1

ProteinName: SNW domain-containing protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.819922 kDa
SourceSpecies: Human (human)

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Component #22: protein, Protein BUD31 homolog

ProteinName: Protein BUD31 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.03285 kDa
SourceSpecies: Human (human)

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Component #23: protein, Pre-mRNA-splicing factor RBM22

ProteinName: Pre-mRNA-splicing factor RBM22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.156129 kDa
SourceSpecies: Human (human)

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Component #24: protein, U5 small nuclear ribonucleoprotein 40 kDa protein

ProteinName: U5 small nuclear ribonucleoprotein 40 kDa protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.09241 kDa
SourceSpecies: Human (human)

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Component #25: protein, Cell division cycle 5-like protein

ProteinName: Cell division cycle 5-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 92.406883 kDa
SourceSpecies: Human (human)

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Component #26: protein, Spliceosome-associated protein CWC15 homolog

ProteinName: Spliceosome-associated protein CWC15 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.674447 kDa
SourceSpecies: Human (human)

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Component #27: protein, Serine/arginine repetitive matrix protein 2

ProteinName: Serine/arginine repetitive matrix protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.767128 kDa
SourceSpecies: Human (human)

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Component #28: protein, Crooked neck-like protein 1

ProteinName: Crooked neck-like protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.610008 kDa
SourceSpecies: Human (human)

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Component #29: protein, Pre-mRNA-splicing factor SYF1

ProteinName: Pre-mRNA-splicing factor SYF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.148711 kDa
SourceSpecies: Human (human)

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Component #30: protein, Intron-binding protein aquarius

ProteinName: Intron-binding protein aquarius / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 171.502453 kDa
SourceSpecies: Human (human)

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Component #31: protein, ATP-dependent RNA helicase DHX8

ProteinName: ATP-dependent RNA helicase DHX8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 139.522312 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #32: protein, U2 small nuclear ribonucleoprotein A'

ProteinName: U2 small nuclear ribonucleoprotein A' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.69773 kDa
SourceSpecies: Human (human)

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Component #33: protein, U2 small nuclear ribonucleoprotein B''

ProteinName: U2 small nuclear ribonucleoprotein B'' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.688563 kDa
SourceSpecies: Human (human)

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Component #34: protein, NF-kappa-B-activating protein

ProteinName: NF-kappa-B-activating protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.321766 kDa
SourceSpecies: Human (human)

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Component #35: protein, Small nuclear ribonucleoprotein-associated proteins B and B'

ProteinName: Small nuclear ribonucleoprotein-associated proteins B and B'
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.551284 kDa
SourceSpecies: Human (human)

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Component #36: protein, Pre-mRNA-splicing factor SLU7

ProteinName: Pre-mRNA-splicing factor SLU7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 68.510844 kDa
SourceSpecies: Human (human)

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Component #37: protein, Small nuclear ribonucleoprotein Sm D3

ProteinName: Small nuclear ribonucleoprotein Sm D3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.460979 kDa
SourceSpecies: Human (human)

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Component #38: protein, Small nuclear ribonucleoprotein E

ProteinName: Small nuclear ribonucleoprotein E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.582185 kDa
SourceSpecies: Human (human)

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Component #39: protein, Small nuclear ribonucleoprotein F

ProteinName: Small nuclear ribonucleoprotein F / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.038415 kDa
SourceSpecies: Human (human)

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Component #40: protein, Small nuclear ribonucleoprotein G

ProteinName: Small nuclear ribonucleoprotein G / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.160629 kDa
SourceSpecies: Human (human)

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Component #41: protein, Small nuclear ribonucleoprotein Sm D1

ProteinName: Small nuclear ribonucleoprotein Sm D1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.086731 kDa
SourceSpecies: Human (human)

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Component #42: protein, Peptidyl-prolyl cis-trans isomerase-like 1

ProteinName: Peptidyl-prolyl cis-trans isomerase-like 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.055529 kDa
SourceSpecies: Human (human)

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Component #43: protein, Small nuclear ribonucleoprotein Sm D2

ProteinName: Small nuclear ribonucleoprotein Sm D2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.551928 kDa
SourceSpecies: Human (human)

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Component #44: protein, Pre-mRNA-processing factor 17

ProteinName: Pre-mRNA-processing factor 17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 59.116055 kDa
SourceSpecies: Human (human)

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Component #45: protein, Pre-mRNA-splicing factor SPF27

ProteinName: Pre-mRNA-splicing factor SPF27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.16342 kDa
SourceSpecies: Human (human)

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Component #46: protein, Pre-mRNA-processing factor 19

ProteinName: Pre-mRNA-processing factor 19 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 55.245547 kDa
SourceSpecies: Human (human)

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Component #47: protein, Pre-mRNA-splicing factor SYF2

ProteinName: Pre-mRNA-splicing factor SYF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.302371 kDa
SourceSpecies: Human (human)

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Component #48: protein, Replication stress response regulator SDE2

ProteinName: Replication stress response regulator SDE2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.036538 kDa
SourceSpecies: Human (human)

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Component #49: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #50: ligand, POTASSIUM ION

LigandName: POTASSIUM IONPotassium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.909805 MDa

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Component #51: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #52: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #53: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #54: ligand, INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE

LigandName: INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.660035 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/mL / pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: 3 uL sample was applied to the grid, left for 25s, then blotted for 2.5-3.5s and immediately plunged into liquid ethane..

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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: 53 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 135000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3500.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 6200

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 103860
3D reconstructionSoftware: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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