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- PDB-8c6j: Human spliceosomal PM5 C* complex -

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Basic information

Entry
Database: PDB / ID: 8c6j
TitleHuman spliceosomal PM5 C* complex
Components
  • (Peptidyl-prolyl cis-trans isomerase-like ...) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 7
  • (Small nuclear ribonucleoprotein ...) x 6
  • (Splicing factor ...) x 3
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • ATP-dependent RNA helicase DHX8
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • Eukaryotic initiation factor 4A-III
  • Intron-binding protein aquarius
  • NF-kappa-B-activating protein
  • Nitric oxide synthase-interacting protein
  • PM5 5' Exon
  • PM5 Intron
  • PRKR-interacting protein 1
  • Peptidyl-prolyl cis-trans isomerase E
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Probable ATP-dependent RNA helicase DDX41
  • Protein BUD31 homolog
  • Protein FAM32A
  • Protein FAM50A
  • Protein mago nashi homolog
  • RNA-binding protein 8A
  • SNW domain-containing protein 1
  • STING ER exit protein
  • Serine/arginine repetitive matrix protein 2
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • Splicing regulator SDE2
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
KeywordsSPLICING / spliceosome / nucleus
Function / homology
Function and homology information


regulation of homologous chromosome segregation / second spliceosomal transesterification activity / endoplasmic reticulum membrane organization / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / negative regulation of nitric-oxide synthase activity / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / post-spliceosomal complex / selenocysteine insertion sequence binding ...regulation of homologous chromosome segregation / second spliceosomal transesterification activity / endoplasmic reticulum membrane organization / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / negative regulation of nitric-oxide synthase activity / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / post-spliceosomal complex / selenocysteine insertion sequence binding / exon-exon junction complex / pre-mRNA 3'-splice site binding / protein exit from endoplasmic reticulum / negative regulation of catalytic activity / NOSIP mediated eNOS trafficking / regulation of translation at postsynapse, modulating synaptic transmission / regulation of retinoic acid receptor signaling pathway / granulocyte differentiation / post-mRNA release spliceosomal complex / renal system process / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / cis assembly of pre-catalytic spliceosome / negative regulation of toll-like receptor signaling pathway / histone pre-mRNA 3'end processing complex / regulation of vitamin D receptor signaling pathway / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of lipopolysaccharide-mediated signaling pathway / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / Deadenylation of mRNA / negative regulation of interleukin-8 production / negative regulation of excitatory postsynaptic potential / embryonic cranial skeleton morphogenesis / alternative mRNA splicing, via spliceosome / U12-type spliceosomal complex / embryonic brain development / nuclear retinoic acid receptor binding / STING mediated induction of host immune responses / protein methylation / poly(A) binding / 7-methylguanosine cap hypermethylation / U1 snRNP binding / negative regulation of interferon-beta production / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / methylosome / pre-mRNA binding / C2H2 zinc finger domain binding / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / ATP-dependent activity, acting on RNA / M-decay: degradation of maternal mRNAs by maternally stored factors / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / sno(s)RNA-containing ribonucleoprotein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / host-mediated activation of viral transcription / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / P granule / positive regulation of vitamin D receptor signaling pathway / commitment complex / snRNP binding / IRF3-mediated induction of type I IFN / telomerase holoenzyme complex / oocyte development / nuclear vitamin D receptor binding / regulation of nitric oxide biosynthetic process / U2-type prespliceosome assembly / Notch binding / U2-type spliceosomal complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / positive regulation of alpha-beta T cell differentiation / Transport of Mature mRNA derived from an Intron-Containing Transcript / telomerase RNA binding / RUNX3 regulates NOTCH signaling / U2-type catalytic step 2 spliceosome / NOTCH4 Intracellular Domain Regulates Transcription / U2 snRNP / U1 snRNP / RNA Polymerase II Transcription Termination / cGAS/STING signaling pathway / : / U4 snRNP / NOTCH3 Intracellular Domain Regulates Transcription / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / U2-type prespliceosome / negative regulation of type I interferon-mediated signaling pathway / positive regulation of neurogenesis / K63-linked polyubiquitin modification-dependent protein binding
Similarity search - Function
XAP5 protein / Nitric oxide synthase-interacting protein / STEEP-like / Nitric oxide synthase-interacting protein, zinc-finger / : / : / XAP5, circadian clock regulator C-terminal domain / Zinc-finger of nitric oxide synthase-interacting protein / STEEP1 domain / Telomere length and silencing protein 1 ...XAP5 protein / Nitric oxide synthase-interacting protein / STEEP-like / Nitric oxide synthase-interacting protein, zinc-finger / : / : / XAP5, circadian clock regulator C-terminal domain / Zinc-finger of nitric oxide synthase-interacting protein / STEEP1 domain / Telomere length and silencing protein 1 / DDX41, DEAD-box helicase domain / Hepatocellular carcinoma-associated antigen 59 / NF-kappa-B-activating protein, C-terminal / NF-kappa-B-activating protein / NF-kappa-B-activating protein C-terminal domain / NF-kappa-B-activating protein / Nuclear protein DGCR14/ESS-2 / : / Nuclear protein Es2 / Vertebrate Splicing regulator sde2, N-terminal ubiquitin domain / Protein FAM32A / Cactin, central domain / Cactin, C-terminal / FAM32A / Cactus-binding C-terminus of cactin protein / Conserved mid region of cactin / PRKR-interacting protein 1 / Protein of unknown function (DUF1168) / : / Splicing regulator SDE2, SDE2 domain / Pre-mRNA-splicing factor SLU7 domain / Pre-mRNA-splicing factor SLU7 / Pre-mRNA splicing Prp18-interacting factor / DHX8/ Prp22, DEXH-box helicase domain / 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 / : / Prp19 WD40 domain / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Peptidyl-prolyl cis-trans isomerase E / : / RBM22 CCCH zinc finger domain / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / 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 / mRNA splicing factor SYF2 / SYF2 splicing factor / Cactus-binding C-terminus of cactin protein / Helix hairpin bin domain superfamily / : / Replication stress response SDE2 C-terminal / : / : / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / mRNA splicing factor Cwf21 domain / cwf21 domain / Pre-mRNA-processing factor 17 / : / 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. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / BUD31/G10-related, conserved site / U-box domain / G10 protein signature 1. / : / STL11, N-terminal / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / : / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / DNA2/NAM7 helicase, helicase domain / AAA domain / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / :
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / Pleiotropic regulator 1 / RNA helicase aquarius / 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' / Small nuclear ribonucleoprotein-associated proteins B and B' / Eukaryotic initiation factor 4A-III / Protein BUD31 homolog / 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 FAM50A / ATP-dependent RNA helicase DHX8 / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing regulator SDE2 / Pre-mRNA-processing-splicing factor 8 / NF-kappa-B-activating protein / Splicing factor Cactin / Splicing factor ESS-2 homolog / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / Crooked neck-like protein 1 / Peptidyl-prolyl cis-trans isomerase-like 3 / STING ER exit protein / PRKR-interacting protein 1 / Pre-mRNA-splicing factor CWC22 homolog / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / Splicing factor C9orf78 / Spliceosome-associated protein CWC15 homolog / Probable ATP-dependent RNA helicase DDX41 / Pre-mRNA-splicing factor ISY1 homolog / Pre-mRNA-processing factor 19 / Peptidyl-prolyl cis-trans isomerase E / Serine/arginine repetitive matrix protein 2 / Nitric oxide synthase-interacting protein / Peptidyl-prolyl cis-trans isomerase-like 1 / Protein FAM32A / RNA-binding protein 8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDybkov, O. / Kastner, B. / Luehrmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Sci Adv / Year: 2023
Title: Regulation of 3' splice site selection after step 1 of splicing by spliceosomal C* proteins.
Authors: Olexandr Dybkov / Marco Preußner / Leyla El Ayoubi / Vivi-Yun Feng / Caroline Harnisch / Kilian Merz / Paula Leupold / Peter Yudichev / Dmitry E Agafonov / Cindy L Will / Cyrille Girard / ...Authors: Olexandr Dybkov / Marco Preußner / Leyla El Ayoubi / Vivi-Yun Feng / Caroline Harnisch / Kilian Merz / Paula Leupold / Peter Yudichev / Dmitry E Agafonov / Cindy L Will / Cyrille Girard / Christian Dienemann / Henning Urlaub / Berthold Kastner / Florian Heyd / Reinhard Lührmann /
Abstract: Alternative precursor messenger RNA splicing is instrumental in expanding the proteome of higher eukaryotes, and changes in 3' splice site (3'ss) usage contribute to human disease. We demonstrate by ...Alternative precursor messenger RNA splicing is instrumental in expanding the proteome of higher eukaryotes, and changes in 3' splice site (3'ss) usage contribute to human disease. We demonstrate by small interfering RNA-mediated knockdowns, followed by RNA sequencing, that many proteins first recruited to human C* spliceosomes, which catalyze step 2 of splicing, regulate alternative splicing, including the selection of alternatively spliced NAGNAG 3'ss. Cryo-electron microscopy and protein cross-linking reveal the molecular architecture of these proteins in C* spliceosomes, providing mechanistic and structural insights into how they influence 3'ss usage. They further elucidate the path of the 3' region of the intron, allowing a structure-based model for how the C* spliceosome potentially scans for the proximal 3'ss. By combining biochemical and structural approaches with genome-wide functional analyses, our studies reveal widespread regulation of alternative 3'ss usage after step 1 of splicing and the likely mechanisms whereby C* proteins influence NAGNAG 3'ss choices.
History
DepositionJan 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_3d_fitting_list.initial_refinement_model_id / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: U2 snRNA
4: Splicing factor ESS-2 homolog
5: U5 snRNA
6: U6 snRNA
7: Eukaryotic initiation factor 4A-III
8: RNA-binding protein 8A
9: Protein mago nashi homolog
A: Pre-mRNA-processing-splicing factor 8
B: U5 small nuclear ribonucleoprotein 200 kDa helicase
C: 116 kDa U5 small nuclear ribonucleoprotein component
C3: Peptidyl-prolyl cis-trans isomerase-like 3
CD: Probable ATP-dependent RNA helicase DDX41
CE: Peptidyl-prolyl cis-trans isomerase E
CF: Protein FAM50A
CI: Pre-mRNA-splicing factor ISY1 homolog
CN: Nitric oxide synthase-interacting protein
CT: Splicing factor C9orf78
D: PRKR-interacting protein 1
E: PM5 5' Exon
F: Splicing factor Cactin
G: Protein FAM32A
H: Pre-mRNA-splicing factor CWC22 homolog
I: PM5 Intron
J: Pleiotropic regulator 1
K: SNW domain-containing protein 1
L: Protein BUD31 homolog
M: Pre-mRNA-splicing factor RBM22
N: U5 small nuclear ribonucleoprotein 40 kDa protein
O: Cell division cycle 5-like protein
P: Spliceosome-associated protein CWC15 homolog
R: Serine/arginine repetitive matrix protein 2
S: Crooked neck-like protein 1
T: Pre-mRNA-splicing factor SYF1
U: Intron-binding protein aquarius
V: ATP-dependent RNA helicase DHX8
W: U2 small nuclear ribonucleoprotein A'
Y: U2 small nuclear ribonucleoprotein B''
Z: NF-kappa-B-activating protein
a: Small nuclear ribonucleoprotein Sm D2
b: Small nuclear ribonucleoprotein-associated proteins B and B'
c: Small nuclear ribonucleoprotein Sm D1
d: Small nuclear ribonucleoprotein Sm D3
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
h: Pre-mRNA-splicing factor SLU7
i: Peptidyl-prolyl cis-trans isomerase-like 1
j: STING ER exit protein
k: Small nuclear ribonucleoprotein-associated proteins B and B'
l: Small nuclear ribonucleoprotein Sm D1
m: Small nuclear ribonucleoprotein Sm D2
n: Small nuclear ribonucleoprotein Sm D3
o: Pre-mRNA-processing factor 17
p: Small nuclear ribonucleoprotein E
q: Small nuclear ribonucleoprotein F
r: Small nuclear ribonucleoprotein G
s: Pre-mRNA-splicing factor SPF27
t: Pre-mRNA-processing factor 19
u: Pre-mRNA-processing factor 19
v: Pre-mRNA-processing factor 19
w: Pre-mRNA-processing factor 19
y: Pre-mRNA-splicing factor SYF2
z: Splicing regulator SDE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,425,22081
Polymers3,422,88963
Non-polymers2,33118
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 5 molecules 256EI

#1: RNA chain U2 snRNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36516
#3: RNA chain U5 snRNA


Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36515
#4: RNA chain U6 snRNA


Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_004394.1
#19: RNA chain PM5 5' Exon


Mass: 78463.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#23: RNA chain PM5 Intron


Mass: 74973.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Splicing factor ... , 3 types, 3 molecules 4CTF

#2: Protein Splicing factor ESS-2 homolog / DiGeorge syndrome critical region 13 / DiGeorge syndrome critical region 14 / DiGeorge syndrome ...DiGeorge syndrome critical region 13 / DiGeorge syndrome critical region 14 / DiGeorge syndrome protein H / DGS-H / Protein ES2


Mass: 52639.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DF8
#17: Protein Splicing factor C9orf78 / Hepatocellular carcinoma-associated antigen 59


Mass: 33751.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZ63
#20: Protein Splicing factor Cactin / Renal carcinoma antigen NY-REN-24


Mass: 88860.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUQ7

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Protein , 24 types, 25 molecules 789ACCDCECFCNDGJKLOPRSUVZbkjz

#5: Protein Eukaryotic initiation factor 4A-III / eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / DEAD box ...eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / DEAD box protein 48 / Eukaryotic initiation factor 4A-like NUK-34 / Eukaryotic translation initiation factor 4A isoform 3 / Nuclear matrix protein 265 / hNMP 265


Mass: 46930.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P38919, RNA helicase
#6: Protein RNA-binding protein 8A / Binder of OVCA1-1 / BOV-1 / RNA-binding motif protein 8A / RNA-binding protein Y14 / Ribonucleoprotein RBM8A


Mass: 19925.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5S9
#7: Protein Protein mago nashi homolog


Mass: 17189.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61326
#8: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#10: Protein 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP- ...Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#12: Protein Probable ATP-dependent RNA helicase DDX41 / DEAD box protein 41 / DEAD box protein abstrakt homolog


Mass: 69943.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UJV9, RNA helicase
#13: Protein Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E


Mass: 33475.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNP9, peptidylprolyl isomerase
#14: Protein Protein FAM50A / Protein HXC-26 / Protein XAP-5


Mass: 40319.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14320
#16: Protein Nitric oxide synthase-interacting protein / E3 ubiquitin-protein ligase NOSIP / RING-type E3 ubiquitin transferase NOSIP / eNOS-interacting protein


Mass: 33224.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9Y314, RING-type E3 ubiquitin transferase
#18: Protein PRKR-interacting protein 1


Mass: 21040.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H875
#21: Protein Protein FAM32A / Ovarian tumor-associated gene 12 / OTAG-12


Mass: 13213.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y421
#24: Protein Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#25: Protein SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61770.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#26: Protein Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#29: Protein Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#30: Protein Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013
#31: Protein Serine/arginine repetitive matrix protein 2 / 300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix ...300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa / Ser/Arg-related nuclear matrix protein of 300 kDa / Splicing coactivator subunit SRm300 / Tax-responsive enhancer element-binding protein 803 / TaxREB803


Mass: 300255.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35
#32: Protein Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 83281.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0
#34: Protein Intron-binding protein aquarius / Intron-binding protein of 160 kDa / IBP160


Mass: 171502.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60306, RNA helicase
#35: Protein ATP-dependent RNA helicase DHX8 / DEAH box protein 8 / RNA helicase HRH1


Mass: 139522.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14562, RNA helicase
#38: Protein NF-kappa-B-activating protein


Mass: 47252.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N5F7
#40: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#48: Protein STING ER exit protein / STEEP


Mass: 25669.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H5V9
#53: Protein Splicing regulator SDE2 / Replication stress response regulator SDE2


Mass: 49818.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6IQ49

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U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules BN

#9: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 ...Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase
#28: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein ...U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57


Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7

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Peptidyl-prolyl cis-trans isomerase-like ... , 2 types, 2 molecules C3i

#11: Protein Peptidyl-prolyl cis-trans isomerase-like 3 / PPIase / Cyclophilin J / CyPJ / Cyclophilin-like protein PPIL3 / Rotamase PPIL3


Mass: 18177.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H2H8, peptidylprolyl isomerase
#47: Protein Peptidyl-prolyl cis-trans isomerase-like 1 / PPIase / Rotamase PPIL1


Mass: 18257.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase

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Pre-mRNA-splicing factor ... , 7 types, 7 molecules CIHMThsy

#15: Protein Pre-mRNA-splicing factor ISY1 homolog


Mass: 33046.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9ULR0
#22: Protein Pre-mRNA-splicing factor CWC22 homolog / Nucampholin homolog / fSAPb


Mass: 57929.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8
#27: Protein Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64
#33: Protein Pre-mRNA-splicing factor SYF1 / Protein HCNP / XPA-binding protein 2


Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7
#46: Protein Pre-mRNA-splicing factor SLU7 / hSlu7


Mass: 68510.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95391
#50: Protein Pre-mRNA-splicing factor SPF27 / Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome- ...Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome-associated protein SPF 27


Mass: 26163.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75934
#52: Protein Pre-mRNA-splicing factor SYF2 / CCNDBP1-interactor / p29


Mass: 28780.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95926

+
U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules WY

#36: Protein U2 small nuclear ribonucleoprotein A' / U2 snRNP A'


Mass: 28456.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09661
#37: Protein U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08579

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Small nuclear ribonucleoprotein ... , 6 types, 12 molecules amcldnepfqgr

#39: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#41: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#42: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#43: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#44: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#45: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

+
Pre-mRNA-processing factor ... , 2 types, 5 molecules otuvw

#49: Protein Pre-mRNA-processing factor 17 / Cell division cycle 40 homolog / EH-binding protein 3 / Ehb3 / PRP17 homolog / hPRP17


Mass: 65612.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60508
#51: Protein
Pre-mRNA-processing factor 19 / Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 ...Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 / Senescence evasion factor


Mass: 55245.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9UMS4, RING-type E3 ubiquitin transferase

+
Non-polymers , 6 types, 18 molecules

#54: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#55: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#56: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#57: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#58: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#59: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: human spliceosomal C* complex assembled on PM5 pre-mRNA
Type: COMPLEX / Entity ID: #1-#53 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.8
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 4 microliter sample was applied to a grid. After 15 s, the grid was blotted for 3 s with a blot force of 5 and vitrified by plunging into liquid ethane using FEI Vitrobot Mark IV.
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.465 sec. / Electron dose: 44.24 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14388

-
Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
7UCSF Chimera1.16model fitting
9PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1643674
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1150057 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDSource nameTypeChain-ID
16QDV

6qdv

6QDV1PDBexperimental model
2AlphaFoldin silico model
37OS2

7os2

B7OS23PDBexperimental modelB
47OS2

7os2

CT7OS23PDBexperimental modelCT
54PJ3

4pj3

U4PJ34PDBexperimental modelU
65MQF

5mqf

I5MQF5PDBexperimental modelI
76BK8

6bk8

I6BK86PDBexperimental modelI
83MDF

3mdf

CE3MDF7PDBexperimental modelCE
95HLY

5hly

CD5HLY8PDBexperimental modelCD
102OK3

2ok3

C32OK39PDBexperimental modelC3
116HYU

6hyu

V6HYU10PDBexperimental modelV

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