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- PDB-7dvq: Cryo-EM Structure of the Activated Human Minor Spliceosome (minor... -

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Basic information

Entry
Database: PDB / ID: 7dvq
TitleCryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)
Components
  • (Pre-mRNA-splicing factor ...) x 2
  • (Serine/arginine repetitive matrix protein ...) x 2
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (Splicing factor 3B subunit ...) x 6
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Armadillo repeat-containing protein 7
  • BUD13 homolog
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • Cysteine-rich PDZ-binding protein
  • G-patch domain and KOW motifs-containing protein
  • PHD finger-like domain-containing protein 5A
  • Peptidyl-prolyl cis-trans isomerase CWC27 homolog
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • RING finger protein 113A
  • RING-type E3 ubiquitin-protein ligase PPIL2
  • RNA-binding motif protein, X-linked 2
  • RNA-binding protein 48
  • SNW domain-containing protein 1
  • Smad nuclear-interacting protein 1
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Sodium channel modifier 1
  • Spliceosome-associated protein CWC15 homolog
  • U12 snRNAU12 minor spliceosomal RNA
  • U5 snRNAU5 spliceosomal RNA
  • U6atac snRNA
  • pre-mRNAPrimary transcript
KeywordsSPLICING / spliceosome / minor spliceosome / Bact complex / human spliceosome / PPIL2 / SCNM1 / RBM48-ARMC7 complex / U12-type intron / U6atac snRNA
Function / homology
Function and homology information


regulation of postsynaptic density protein 95 clustering / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / post-mRNA release spliceosomal complex / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / protein localization to microtubule / U2 snRNP binding / U7 snRNA binding ...regulation of postsynaptic density protein 95 clustering / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / post-mRNA release spliceosomal complex / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / protein localization to microtubule / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / alternative mRNA splicing, via spliceosome / regulation of vitamin D receptor signaling pathway / B-WICH complex / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / miRNA processing / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / mRNA 3'-end processing / blastocyst formation / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / P granule / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / telomerase RNA binding / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / commitment complex / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / transcription regulator inhibitor activity / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / nuclear vitamin D receptor binding / Notch binding / U4 snRNP / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / SAGA complex / RUNX3 regulates NOTCH signaling / Basigin interactions / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / RHOBTB1 GTPase cycle / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / pattern recognition receptor activity / positive regulation of neurogenesis / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / precatalytic spliceosome / spliceosomal complex assembly / Notch-HLH transcription pathway / positive regulation of transcription by RNA polymerase I / Formation of paraxial mesoderm / mRNA Splicing - Minor Pathway / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / regulation of RNA splicing / antiviral innate immune response / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / positive regulation of G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / U5 snRNA binding / U5 snRNP / RHOBTB2 GTPase cycle / localization / U2 snRNA binding / RNA processing / Cajal body / U6 snRNA binding / spliceosomal snRNP assembly
Similarity search - Function
RBM48, RNA recognition motif / RNA-binding protein 48 / Armadillo repeat-containing protein 7 / Sodium channel modifier 1, zinc-finger / Sodium channel modifier 1, acidic C-terminal domain / Sodium channel modifier 1 / Zinc-finger of sodium channel modifier 1 / Acidic C-terminal region of sodium channel modifier 1 SCNM1 / G-patch domain and KOW motifs-containing protein, KOW 1 / G-patch domain and KOW motifs-containing protein, KOW 2 ...RBM48, RNA recognition motif / RNA-binding protein 48 / Armadillo repeat-containing protein 7 / Sodium channel modifier 1, zinc-finger / Sodium channel modifier 1, acidic C-terminal domain / Sodium channel modifier 1 / Zinc-finger of sodium channel modifier 1 / Acidic C-terminal region of sodium channel modifier 1 SCNM1 / G-patch domain and KOW motifs-containing protein, KOW 1 / G-patch domain and KOW motifs-containing protein, KOW 2 / Peptidyl-prolyl cis-trans isomerase like 2, U-box domain / PDZ-binding protein, CRIPT / Microtubule-associated protein CRIPT / Pre-mRNA-splicing factor Spp2-like / Spp2/MOS2, G-patch domain / Pre-mRNA-splicing factor CWC24-like / G-patch domain / Ist3-like, RNA recognition motif / Bud13 / Pre-mRNA-splicing factor of RES complex / : / SF3B6, RNA recognition motif / SF3B4, RNA recognition motif 2 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / PWI domain superfamily / PWI domain / PWI domain profile. / mRNA splicing factor Cwf21 domain / cwf21 domain / G-patch domain profile. / WD repeat Prp46/PLRG1-like / PWI domain / SF3B4, RNA recognition motif 1 / PWI, domain in splicing factors / : / : / G-patch domain / glycine rich nucleic binding domain / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Splicing factor 3B, subunit 5 / Myb-like DNA-binding domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / HAT (Half-A-TPR) repeat / Cwf15/Cwc15 cell cycle control protein / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / pre-mRNA splicing factor component / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / PHF5-like / MIF4G domain / PHF5-like protein / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Small ribonucleoprotein associated, SmB/SmN / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Splicing factor 3B subunit 1-like / Small nuclear ribonucleoprotein D1 / U-box domain profile. / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Modified RING finger domain / U-box domain / Zinc finger, CCCH-type superfamily / : / Helicase associated domain (HA2), ratchet-like / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / zinc finger / SAP domain / Pre-mRNA-splicing factor Syf1-like / SAP motif profile. / Sec63 Brl domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Snu114, GTP-binding domain / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2
Similarity search - Domain/homology
Chem-G5J / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...Chem-G5J / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / Splicing factor 3B subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Small nuclear ribonucleoprotein-associated proteins B and B' / 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 / RING-type E3 ubiquitin-protein ligase PPIL2 / Splicing factor 3B subunit 2 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3B subunit 3 / Splicing factor 3B subunit 4 / RNA-binding protein 48 / Pre-mRNA-processing-splicing factor 8 / Spliceosome-associated protein CWC27 homolog / PHD finger-like domain-containing protein 5A / Serine/arginine repetitive matrix protein 1 / Smad nuclear-interacting protein 1 / G-patch domain and KOW motifs-containing protein / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / BUD13 homolog / Sodium channel modifier 1 / Splicing factor 3B subunit 5 / Crooked neck-like protein 1 / Armadillo repeat-containing protein 7 / Pre-mRNA-splicing factor CWC22 homolog / Spliceosome-associated protein CWC15 homolog / Cysteine-rich PDZ-binding protein / Serine/arginine repetitive matrix protein 2 / RNA-binding motif protein, X-linked 2 / Splicing factor 3B subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsBai, R. / Wan, R. / Wang, L. / Xu, K. / Zhang, Q. / Lei, J. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Science / Year: 2021
Title: Structure of the activated human minor spliceosome.
Authors: Rui Bai / Ruixue Wan / Lin Wang / Kui Xu / Qiangfeng Zhang / Jianlin Lei / Yigong Shi /
Abstract: The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. Here, we report the atomic features of the activated human minor spliceosome determined by cryo- ...The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. Here, we report the atomic features of the activated human minor spliceosome determined by cryo-electron microscopy at 2.9-angstrom resolution. The 5' splice site and branch point sequence of the U12-type intron are recognized by the U6atac and U12 small nuclear RNAs (snRNAs), respectively. Five newly identified proteins stabilize the conformation of the catalytic center: The zinc finger protein SCNM1 functionally mimics the SF3a complex of the major spliceosome, the RBM48-ARMC7 complex binds the γ-monomethyl phosphate cap at the 5' end of U6atac snRNA, the U-box protein PPIL2 coordinates loop I of U5 snRNA and stabilizes U5 small nuclear ribonucleoprotein (snRNP), and CRIPT stabilizes U12 snRNP. Our study provides a framework for the mechanistic understanding of the function of the human minor spliceosome.
History
DepositionJan 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: U5 snRNA
C: 116 kDa U5 small nuclear ribonucleoprotein component
D: U5 small nuclear ribonucleoprotein 200 kDa helicase
E: U5 small nuclear ribonucleoprotein 40 kDa protein
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
f: Small nuclear ribonucleoprotein F
e: Small nuclear ribonucleoprotein E
g: Small nuclear ribonucleoprotein G
F: U6atac snRNA
G: pre-mRNA
H: U12 snRNA
h: Small nuclear ribonucleoprotein Sm D3
i: Small nuclear ribonucleoprotein-associated proteins B and B'
j: Small nuclear ribonucleoprotein Sm D1
k: Small nuclear ribonucleoprotein Sm D2
m: Small nuclear ribonucleoprotein F
l: Small nuclear ribonucleoprotein E
n: Small nuclear ribonucleoprotein G
v: Sodium channel modifier 1
1: Splicing factor 3B subunit 1
2: Splicing factor 3B subunit 2
3: Splicing factor 3B subunit 3
4: Splicing factor 3B subunit 4
5: Splicing factor 3B subunit 6
6: PHD finger-like domain-containing protein 5A
7: Splicing factor 3B subunit 5
L: Cell division cycle 5-like protein
J: Crooked neck-like protein 1
P: Spliceosome-associated protein CWC15 homolog
R: SNW domain-containing protein 1
T: Pleiotropic regulator 1
X: Smad nuclear-interacting protein 1
Y: RNA-binding motif protein, X-linked 2
Z: BUD13 homolog
9: RING-type E3 ubiquitin-protein ligase PPIL2
z: Peptidyl-prolyl cis-trans isomerase CWC27 homolog
x: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
y: G-patch domain and KOW motifs-containing protein
M: RING finger protein 113A
U: Serine/arginine repetitive matrix protein 2
V: Pre-mRNA-splicing factor CWC22 homolog
8: Serine/arginine repetitive matrix protein 1
0: Cysteine-rich PDZ-binding protein
I: RNA-binding protein 48
K: Armadillo repeat-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,918,37666
Polymers2,915,99849
Non-polymers2,37817
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 20 types, 21 molecules ACbiv6LJPRTXYZ9zyM0IK

#1: 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
#3: 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 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
#16: Protein Sodium channel modifier 1


Mass: 25993.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWG6
#22: Protein PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b


Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7RTV0
#24: 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
#25: 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
#26: 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
#27: Protein SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61610.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#28: 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
#29: Protein Smad nuclear-interacting protein 1 / FHA domain-containing protein SNIP1


Mass: 45880.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAD8
#30: Protein RNA-binding motif protein, X-linked 2


Mass: 37425.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y388
#31: Protein BUD13 homolog


Mass: 70669.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRD0
#32: Protein RING-type E3 ubiquitin-protein ligase PPIL2 / CYC4 / Cyclophilin-60 / Cyclophilin-like protein Cyp-60 / Cyp60 / hCyP-60 / Probable inactive ...CYC4 / Cyclophilin-60 / Cyclophilin-like protein Cyp-60 / Cyp60 / hCyP-60 / Probable inactive peptidyl-prolyl cis-trans isomerase-like 2 / PPIase / Rotamase PPIL2


Mass: 58910.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q13356, RING-type E3 ubiquitin transferase
#33: Protein Peptidyl-prolyl cis-trans isomerase CWC27 homolog / PPIase CWC27 / Antigen NY-CO-10 / Serologically defined colon cancer antigen 10


Mass: 53941.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6UX04, peptidylprolyl isomerase
#35: Protein G-patch domain and KOW motifs-containing protein / G-patch domain-containing protein 5 / Protein MOS2 homolog / Protein T54


Mass: 52299.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92917
#36: Protein RING finger protein 113A / / Zinc finger protein 183


Mass: 38847.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15541
#40: Protein Cysteine-rich PDZ-binding protein / Cysteine-rich interactor of PDZ three / Cysteine-rich interactor of PDZ3


Mass: 11239.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P021
#41: Protein RNA-binding protein 48


Mass: 41878.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5RL73
#42: Protein Armadillo repeat-containing protein 7


Mass: 21946.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H6L4

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RNA chain , 4 types, 4 molecules BFGH

#2: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981
#13: RNA chain U6atac snRNA


Mass: 39876.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 187960111
#14: RNA chain pre-mRNA / Primary transcript


Mass: 44322.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#15: RNA chain U12 snRNA / U12 minor spliceosomal RNA


Mass: 48353.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 951206

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

#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
#5: 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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Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahcjdkfmelgn

#6: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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

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Splicing factor 3B subunit ... , 6 types, 6 molecules 123457

#17: Protein Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155


Mass: 146104.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75533
#18: Protein Splicing factor 3B subunit 2 / Pre-mRNA-splicing factor SF3b 145 kDa subunit / SF3b145 / Spliceosome-associated protein 145 / SAP 145


Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13435
#19: Protein Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


Mass: 135798.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393
#20: Protein Splicing factor 3B subunit 4 / Pre-mRNA-splicing factor SF3b 49 kDa subunit / Spliceosome-associated protein 49 / SAP 49


Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15427
#21: Protein Splicing factor 3B subunit 6 / Pre-mRNA branch site protein p14 / SF3b 14 kDa subunit / SF3B14a / Spliceosome-associated protein / ...Pre-mRNA branch site protein p14 / SF3b 14 kDa subunit / SF3B14a / Spliceosome-associated protein / 14-kDa / Splicing factor 3b / subunit 6 / 14kDa


Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B4
#23: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWJ5

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Pre-mRNA-splicing factor ... , 2 types, 2 molecules xV

#34: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / ATP-dependent RNA helicase #3 / DEAH-box protein 16


Mass: 119443.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60231, RNA helicase
#38: Protein Pre-mRNA-splicing factor CWC22 homolog / Nucampholin homolog / fSAPb


Mass: 105646.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8

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Serine/arginine repetitive matrix protein ... , 2 types, 2 molecules U8

#37: 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
#39: Protein Serine/arginine repetitive matrix protein 1 / SR-related nuclear matrix protein of 160 kDa / SRm160 / Ser/Arg-related nuclear matrix protein


Mass: 102600.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IYB3

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Non-polymers , 7 types, 20 molecules

#43: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


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


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#46: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#47: Chemical ChemComp-G5J / 5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine


Mass: 537.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#48: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#49: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: the activated human minor spliceosome (human minor Bact complex)
Type: COMPLEX / Entity ID: #1-#12, #14-#42 / Source: NATURAL
Molecular weightExperimental value: NO
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101443 / Symmetry type: POINT

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