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- PDB-9xtt: Human minor spliceosome branching-completed C complex (after step-I) -

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Basic information

Entry
Database: PDB / ID: 9xtt
TitleHuman minor spliceosome branching-completed C complex (after step-I)
Components
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Pre-mRNA-splicing factor ...) x 7
  • (RNA-binding protein ...) x 2
  • (Small nuclear ribonucleoprotein ...) x 6
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • (Unknown polymer) x 3
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Armadillo repeat-containing protein 7
  • Cell division cycle 5-like protein
  • Coiled-coil domain-containing protein 12
  • Crooked neck-like protein 1
  • Eukaryotic initiation factor 4A-III
  • MSE-U12_Intron
  • MSE-U12_exon
  • Multiple myeloma tumor-associated protein 2
  • Peptidylprolyl isomerase domain and WD repeat-containing protein 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing factor 19
  • Pre-mRNA-processing-splicing factor 8
  • Protein FRG1
  • Protein mago nashi homolog
  • RNA helicase aquarius
  • SNW domain-containing protein 1
  • Serine/arginine repetitive matrix protein 2
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • Splicing factor YJU2
  • U12 snRNA
  • U5 snRNA
  • U6atac snRNA
  • WD repeat-containing protein 70
KeywordsSPLICING / minor spliceosome / U12-dependent spliceosome / U12-type splicing / step-I spliceosome / branching / snRNP / U12 / U5 / U6atac / intron lariat
Function / homology
Function and homology information


second spliceosomal transesterification activity / striated muscle dense body / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / cellular response to selenite ion / post-spliceosomal complex / exon-exon junction complex / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of vitamin D receptor signaling pathway / pre-mRNA 3'-splice site binding ...second spliceosomal transesterification activity / striated muscle dense body / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / cellular response to selenite ion / post-spliceosomal complex / exon-exon junction complex / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of vitamin D receptor signaling pathway / pre-mRNA 3'-splice site binding / selenocysteine insertion sequence binding / mRNA metabolic process / regulation of translation at postsynapse, modulating synaptic transmission / regulation of retinoic acid receptor signaling pathway / alternative mRNA splicing, via spliceosome / 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 / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / cis assembly of pre-catalytic spliceosome / histone pre-mRNA 3'end processing complex / nuclear histone mRNA catabolic process / embryonic cranial skeleton morphogenesis / SLBP independent Processing of Histone Pre-mRNAs / regulation of mRNA processing / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Deadenylation of mRNA / negative regulation of excitatory postsynaptic potential / embryonic brain development / poly(A) binding / 7-methylguanosine cap hypermethylation / U12-type spliceosomal complex / positive regulation of mRNA splicing, via spliceosome / nuclear retinoic acid receptor binding / U1 snRNP binding / C2H2 zinc finger domain binding / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / methylosome / regulation of mRNA splicing, via spliceosome / RNA splicing, via transesterification reactions / mRNA 3'-end processing / sno(s)RNA-containing ribonucleoprotein complex / small nuclear ribonucleoprotein complex / M-decay: degradation of maternal mRNAs by maternally stored factors / SMN-Sm protein complex / spliceosomal tri-snRNP complex / positive regulation of vitamin D receptor signaling pathway / commitment complex / P granule / 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 / U2-type prespliceosome assembly / RUNX3 regulates NOTCH signaling / U2-type catalytic step 2 spliceosome / Notch binding / U2-type spliceosomal complex / nuclear vitamin D receptor binding / telomerase holoenzyme complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / NOTCH4 Intracellular Domain Regulates Transcription / telomerase RNA binding / exploration behavior / positive regulation of neurogenesis / U1 snRNP / U2 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / RNA Polymerase II Transcription Termination / NOTCH3 Intracellular Domain Regulates Transcription / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / protein methylation / mRNA stabilization / U2-type prespliceosome / muscle organ development / protein peptidyl-prolyl isomerization / K63-linked polyubiquitin modification-dependent protein binding / 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 / regulation of alternative mRNA splicing, via spliceosome / positive regulation of transforming growth factor beta receptor signaling pathway / WD40-repeat domain binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / 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
Similarity search - Function
Multiple myeloma tumor-associated protein 2-like, N-terminal / Multiple myeloma tumor-associated protein 2-like / Multiple myeloma tumor-associated / RBM48, RNA recognition motif / RNA-binding protein 48 / Armadillo repeat-containing protein 7 / : / : / RNA-binding protein 48 helical domain / Protein FRG1 ...Multiple myeloma tumor-associated protein 2-like, N-terminal / Multiple myeloma tumor-associated protein 2-like / Multiple myeloma tumor-associated / RBM48, RNA recognition motif / RNA-binding protein 48 / Armadillo repeat-containing protein 7 / : / : / RNA-binding protein 48 helical domain / Protein FRG1 / FRG1-like domain / CBF1-interacting co-repressor CIR, N-terminal domain / Pre-mRNA splicing factor / : / N-terminal domain of CBF1 interacting co-repressor CIR / Pre-mRNA splicing factor / N-terminal domain of CBF1 interacting co-repressor CIR / mRNA splicing factor Cwf18-like / Splicing factor Yju2 / cwf18 pre-mRNA splicing factor / Saf4/Yju2 protein / Saf4/Yju2 protein / Pre-mRNA-splicing factor SLU7 domain / Pre-mRNA-splicing factor SLU7 / Pre-mRNA splicing Prp18-interacting factor / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / Actin-crosslinking / 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 / 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 / Helix hairpin bin domain superfamily / : / : / mRNA splicing factor Cwf21 domain / cwf21 domain / UPF1-type helicase core domain profile. / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / : / Prp19/Pso4-like / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / 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 / : / Initiation factor eIF-4 gamma, MA3 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / : / MA3 domain / pre-mRNA splicing factor component / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / DNA2/NAM7-like helicase / : / MIF4G domain / Small ribonucleoprotein associated, SmB/SmN / Myb-like DNA-binding domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / 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.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / Pleiotropic regulator 1 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / Pleiotropic regulator 1 / RNA helicase aquarius / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-splicing factor SPF27 / Pre-mRNA-splicing factor SLU7 / Small nuclear ribonucleoprotein-associated proteins B and B' / Eukaryotic initiation factor 4A-III / 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 FRG1 / 116 kDa U5 small nuclear ribonucleoprotein component / RNA-binding protein 48 / Pre-mRNA-processing-splicing factor 8 / Coiled-coil domain-containing protein 12 / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / Peptidylprolyl isomerase domain and WD repeat-containing protein 1 / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / Multiple myeloma tumor-associated protein 2 / Splicing factor YJU2 / Crooked neck-like protein 1 / Armadillo repeat-containing protein 7 / Pre-mRNA-splicing factor CWC22 homolog / Pre-mRNA-splicing factor SYF1 / WD repeat-containing protein 70 / Pre-mRNA-splicing factor CWC25 homolog / Spliceosome-associated protein CWC15 homolog / Pre-mRNA-splicing factor ISY1 homolog / Pre-mRNA-processing factor 19 / Peptidyl-prolyl cis-trans isomerase E / Serine/arginine repetitive matrix protein 2 / Peptidyl-prolyl cis-trans isomerase-like 1 / RNA-binding protein 8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsBai, R. / Wan, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171214 China
CitationJournal: Vita / Year: 2026
Title: Molecular mechanism of the catalysis for U12-type splicing by the human
Authors: Bai, R. / Guo, H. / Sun, R. / Zhu, Y. / Shi, Y. / Wan, R.
History
DepositionNov 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: MSE-U12_exon
1: MSE-U12_Intron
2: U12 snRNA
4: Peptidylprolyl isomerase domain and WD repeat-containing protein 1
5: U5 snRNA
6: U6atac snRNA
A: Pre-mRNA-processing-splicing factor 8
B: 116 kDa U5 small nuclear ribonucleoprotein component
C: U5 small nuclear ribonucleoprotein 200 kDa helicase
D: U5 small nuclear ribonucleoprotein 40 kDa protein
E: Cell division cycle 5-like protein
F: Pre-mRNA-splicing factor SYF1
G: Crooked neck-like protein 1
H: Coiled-coil domain-containing protein 12
I: Pre-mRNA-splicing factor ISY1 homolog
J: SNW domain-containing protein 1
K: Pleiotropic regulator 1
L: RNA-binding protein 48
M: Armadillo repeat-containing protein 7
N: Spliceosome-associated protein CWC15 homolog
O: Peptidyl-prolyl cis-trans isomerase-like 1
P: Peptidyl-prolyl cis-trans isomerase E
Q: RNA helicase aquarius
R: Pre-mRNA-splicing factor CWC25 homolog
S: Pre-mRNA-splicing factor SLU7
T: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
U: Serine/arginine repetitive matrix protein 2
V: Pre-mRNA-splicing factor CWC22 homolog
X: Protein FRG1
X1: Unknown polymer
X2: Unknown polymer
X3: Unknown polymer
Y: Splicing factor YJU2
Z: WD repeat-containing protein 70
a: Small nuclear ribonucleoprotein-associated proteins B and B'
b: Small nuclear ribonucleoprotein Sm D1
c: Small nuclear ribonucleoprotein Sm D2
d: Small nuclear ribonucleoprotein Sm D3
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
h: Small nuclear ribonucleoprotein-associated proteins B and B'
i: Small nuclear ribonucleoprotein Sm D1
j: Small nuclear ribonucleoprotein Sm D2
k: Small nuclear ribonucleoprotein Sm D3
l: Small nuclear ribonucleoprotein E
m: Small nuclear ribonucleoprotein F
n: 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
u: Pre-mRNA-splicing factor SPF27
v: Eukaryotic initiation factor 4A-III
w: Protein mago nashi homolog
x: RNA-binding protein 8A
z: Multiple myeloma tumor-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,117,42375
Polymers3,114,45057
Non-polymers2,97318
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules 01256

#1: RNA chain MSE-U12_exon


Mass: 18256.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: RNA chain MSE-U12_Intron


Mass: 88640.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: RNA chain U12 snRNA


Mass: 48353.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#5: RNA chain U5 snRNA


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


Mass: 40395.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein , 20 types, 24 molecules 4ABEGHJKMNQUXYZahqrstvwz

#4: Protein Peptidylprolyl isomerase domain and WD repeat-containing protein 1 / Spliceosome-associated cyclophilin


Mass: 73679.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP3, peptidylprolyl isomerase
#7: 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
#8: 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
#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 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
#14: 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
#16: Protein SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61690.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#17: 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
#19: 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
#20: 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
#23: Protein RNA helicase 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
#27: 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 / SR-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
#29: Protein Protein FRG1 / FSHD region gene 1 protein


Mass: 29227.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14331
#33: Protein Splicing factor YJU2 / Coiled-coil domain-containing protein 94


Mass: 39867.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BW85
#34: Protein WD repeat-containing protein 70


Mass: 73306.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW82
#35: 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.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#42: 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
#44: Protein Eukaryotic initiation factor 4A-III / eIF-4A-III / eIF4A-III / ATP-dependent RNA helicase DDX48 / ATP-dependent RNA helicase eIF4A-3 / ...eIF-4A-III / 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 / NMP 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
#45: 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
#47: Protein Multiple myeloma tumor-associated protein 2 / hMMTAG2


Mass: 29486.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BU76

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

#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
#10: 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 ... , 7 types, 7 molecules FIRSTVu

#12: 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
#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
#24: Protein Pre-mRNA-splicing factor CWC25 homolog / Coiled-coil domain-containing protein 49 / Spliceosome-associated protein homolog CWC25


Mass: 49769.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NXE8
#25: 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
#26: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / ATP-dependent RNA helicase DHX38 / DEAH box protein 38


Mass: 140662.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX38, DDX38, KIAA0224, PRP16 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q92620, RNA helicase
#28: 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
#43: 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

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RNA-binding protein ... , 2 types, 2 molecules Lx

#18: 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
#46: 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

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

#21: 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
#22: 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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Protein/peptide , 3 types, 3 molecules X1X2X3

#30: Protein/peptide Unknown polymer


Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: RNA helicase
#31: Protein/peptide Unknown polymer


Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: RNA helicase
#32: Protein/peptide Unknown polymer


Mass: 1805.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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

#36: 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
#37: 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
#38: 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
#39: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-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
#40: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-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
#41: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-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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Non-polymers , 7 types, 18 molecules

#48: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#49: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#50: 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
#51: 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
#52: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#53: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#54: 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

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Details

Has ligand of interestY
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: Human minor spliceosome branching-completed C complex (after step-I)
Type: COMPLEX
Entity ID: #1-#2, #5, #7-#8, #10, #38, #35-#37, #39-#41, #6, #3, #42-#43, #11-#13, #15-#17, #20-#21, #23, #22, #44-#46, #24, #33, #26, #28-#29, #47, #18-#19, #34, #14, #4, #25
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86306 / Symmetry type: POINT

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