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- PDB-9s2f: Human debranched intron spliceosome (DIS) -

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Basic information

Entry
Database: PDB / ID: 9s2f
TitleHuman debranched intron spliceosome (DIS)
Components
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 5
  • (Small nuclear ribonucleoprotein ...) x 6
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Cell division cycle 5-like protein
  • Coiled-coil domain-containing protein 12
  • Crooked neck-like protein 1
  • G patch domain-containing protein 1
  • Intron
  • Intron-binding protein aquarius
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Probable ATP-dependent RNA helicase DHX35
  • Protein BUD31 homolog
  • SNW domain-containing protein 1
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • U5 snRNA
  • U6 snRNA
  • WD repeat domain-containing protein 83
KeywordsSPLICING / Spliceosome / complex
Function / homology
Function and homology information


post-spliceosomal complex / regulation of vitamin D receptor signaling pathway / oocyte development / regulation of retinoic acid receptor signaling pathway / blastocyst development / post-mRNA release spliceosomal complex / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step ...post-spliceosomal complex / regulation of vitamin D receptor signaling pathway / oocyte development / regulation of retinoic acid receptor signaling pathway / blastocyst development / post-mRNA release spliceosomal complex / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / 3'-5' RNA helicase activity / cis assembly of pre-catalytic spliceosome / histone pre-mRNA 3'end processing complex / nuclear histone mRNA catabolic process / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / inner cell mass cell proliferation / alternative mRNA splicing, via spliceosome / poly(A) binding / 7-methylguanosine cap hypermethylation / U12-type spliceosomal complex / nuclear retinoic acid receptor binding / embryonic brain development / positive regulation of mRNA splicing, via spliceosome / U1 snRNP binding / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / methylosome / RNA splicing, via transesterification reactions / mRNA 3'-end processing / sno(s)RNA-containing ribonucleoprotein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / protein methylation / spliceosomal tri-snRNP complex / positive regulation of vitamin D receptor signaling pathway / P granule / commitment complex / U4 snRNP / snRNP binding / host-mediated activation of viral transcription / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Notch binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U2-type spliceosomal complex / nuclear vitamin D receptor binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / NOTCH4 Intracellular Domain Regulates Transcription / telomerase holoenzyme complex / telomerase RNA binding / pre-mRNA binding / positive regulation of neurogenesis / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U1 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH3 Intracellular Domain Regulates Transcription / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / protein peptidyl-prolyl isomerization / nuclear androgen receptor binding / cyclosporin A binding / generation of catalytic spliceosome for second transesterification step / precatalytic spliceosome / ubiquitin-ubiquitin ligase activity / Notch-HLH transcription pathway / Formation of paraxial mesoderm / lipid biosynthetic process / WD40-repeat domain binding / positive regulation of transforming growth factor beta receptor signaling pathway / mRNA 3'-splice site recognition / SMAD binding / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Prp19 complex / negative regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex assembly / U5 snRNP / U5 snRNA binding / ovarian follicle development / pre-mRNA intronic binding / U2 snRNA binding / U6 snRNA binding / protein localization to nucleus / positive regulation of G1/S transition of mitotic cell cycle / Cajal body / U1 snRNA binding / protein K63-linked ubiquitination / retinoic acid receptor signaling pathway / RNA processing / U4/U6 x U5 tri-snRNP complex / positive regulation of viral genome replication / cellular response to retinoic acid / spliceosomal snRNP assembly
Similarity search - Function
: / TGH-like, helix-turn-helix domain / G patch domain-containing protein, N-terminal / G patch domain-containing protein, N-terminal / mRNA splicing factor Cwf18-like / cwf18 pre-mRNA splicing factor / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / Prp19 WD40 domain ...: / TGH-like, helix-turn-helix domain / G patch domain-containing protein, N-terminal / G patch domain-containing protein, N-terminal / mRNA splicing factor Cwf18-like / cwf18 pre-mRNA splicing factor / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / Prp19 WD40 domain / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / : / RBM22 CCCH zinc finger domain / 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 / Helix hairpin bin domain superfamily / G-patch domain / G-patch domain profile. / 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 / G-patch domain / G10 protein signature 2. / BUD31/G10-related, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / G10 protein signature 1. / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / : / STL11, N-terminal / DNA2/NAM7 helicase, helicase domain / AAA domain / U-box domain / SKI-interacting protein SKIP, SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / SKI-interacting protein, SKIP / SKIP/SNW domain / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / : / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / : / pre-mRNA splicing factor component / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / G10 protein / Pre-mRNA-splicing factor BUD31 / DNA2/NAM7-like helicase / : / Small ribonucleoprotein associated, SmB/SmN / Myb-like DNA-binding domain / Small nuclear ribonucleoprotein D1 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / : / Winged Helix-turn-helix domain / Sec63 Brl domain / U-box domain profile. / Zinc finger, CCCH-type superfamily / : / Pre-mRNA-splicing factor Syf1-like / zinc finger / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Modified RING finger domain / U-box domain / Sec63 domain / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D2 / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Small nuclear ribonucleoprotein Sm D3 / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Small nuclear ribonucleoprotein E / Helicase associated domain (HA2) Add an annotation / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / Pleiotropic regulator 1 / RNA helicase aquarius / Pre-mRNA-processing factor 17 ...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 SYF2 / Small nuclear ribonucleoprotein-associated proteins B and B' / Protein BUD31 homolog / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Pre-mRNA-processing-splicing factor 8 / Coiled-coil domain-containing protein 12 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / G patch domain-containing protein 1 / WD repeat domain-containing protein 83 / Crooked neck-like protein 1 / Probable ATP-dependent RNA helicase DHX35 / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-splicing factor ISY1 homolog / Pre-mRNA-processing factor 19 / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsBoreikaite, V. / Vorlaender, M.K. / Plaschka, C.
Funding supportEuropean Union, France, Austria, 5items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 784-2023European Union
Human Frontier Science Program (HFSP)LT0013/2024-L France
Austrian Science FundESP7844224 Austria
European Research Council (ERC)ERC-2020-STG 949081European Union
Austrian Science FundDOC177-B Austria
Citation
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
35: Probable ATP-dependent RNA helicase DHX35
5: U5 snRNA
A: Pre-mRNA-processing-splicing factor 8
B: U5 small nuclear ribonucleoprotein 200 kDa helicase
C: 116 kDa U5 small nuclear ribonucleoprotein component
E: U5 small nuclear ribonucleoprotein 40 kDa protein
GP: G patch domain-containing protein 1
I: Pre-mRNA-splicing factor SYF1
J: Crooked neck-like protein 1
K: Pre-mRNA-splicing factor SPF27
L: Cell division cycle 5-like protein
M: Pre-mRNA-splicing factor SYF2
N: Protein BUD31 homolog
O: Pre-mRNA-splicing factor RBM22
P: Spliceosome-associated protein CWC15 homolog
Q: Intron-binding protein aquarius
R: SNW domain-containing protein 1
S: Peptidyl-prolyl cis-trans isomerase-like 1
T: Pleiotropic regulator 1
W: Pre-mRNA-processing factor 17
WD: WD repeat domain-containing protein 83
Z: Coiled-coil domain-containing protein 12
a: Small nuclear ribonucleoprotein Sm D3
b: Small nuclear ribonucleoprotein-associated proteins B and B'
c: Small nuclear ribonucleoprotein Sm D1
d: Small nuclear ribonucleoprotein Sm D2
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
y: Peptidyl-prolyl cis-trans isomerase E
D: Pre-mRNA-splicing factor ISY1 homolog
IN: Intron
6: U6 snRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,174,48843
Polymers2,173,08537
Non-polymers1,4046
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 14 types, 14 molecules 35ACGPJLNPQRTWDZb

#1: Protein Probable ATP-dependent RNA helicase DHX35 / DEAH box protein 35


Mass: 79012.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H5Z1, RNA helicase
#3: 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
#5: 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
#7: Protein G patch domain-containing protein 1 / Evolutionarily conserved G-patch domain-containing protein


Mass: 103514.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRR8
#9: Protein Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0
#11: 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
#13: 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
#15: 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
#16: 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
#17: 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
#19: 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
#21: Protein WD repeat domain-containing protein 83 / Mitogen-activated protein kinase organizer 1 / MAPK organizer 1


Mass: 34383.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRX9
#22: Protein Coiled-coil domain-containing protein 12


Mass: 19223.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUD4
#24: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / Sm-B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678

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RNA chain , 3 types, 3 molecules 5IN6

#2: 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
#33: RNA chain Intron


Mass: 3016.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#34: 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

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

#4: 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
#6: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / U5 snRNP 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 ...U5 snRNP 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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Pre-mRNA-splicing factor ... , 5 types, 5 molecules IKMOD

#8: 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
#10: 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
#12: 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
#14: 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
#32: 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

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Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules Sy

#18: 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
#31: 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

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Pre-mRNA-processing factor ... , 2 types, 5 molecules Wqrst

#20: 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
#30: 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

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Small nuclear ribonucleoprotein ... , 6 types, 6 molecules acdefg

#23: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#25: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#26: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#27: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE


Mass: 10817.601 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#28: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#29: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG


Mass: 8508.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

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Non-polymers , 4 types, 6 molecules

#35: 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
#36: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#37: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#38: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Debranched intron spliceosome complex / Type: COMPLEX / Entity ID: #1-#2, #34, #3-#8, #33, #9-#32 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2250 nm / Nominal defocus min: 1250 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419+SVNmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153470 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 153.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008878854
ELECTRON MICROSCOPYf_angle_d1.0661108384
ELECTRON MICROSCOPYf_chiral_restr0.082512754
ELECTRON MICROSCOPYf_plane_restr0.010213947
ELECTRON MICROSCOPYf_dihedral_angle_d13.204227016

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