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- PDB-8i0w: The cryo-EM structure of human C complex -

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Entry
Database: PDB / ID: 8i0w
TitleThe cryo-EM structure of human C complex
Components
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 8
  • (Small nuclear ribonucleoprotein ...) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • (pre-mRNA) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Cell division cycle 5-like protein
  • Coiled-coil domain-containing protein 94
  • Corepressor interacting with RBPJ 1
  • Crooked neck-like protein 1
  • Eukaryotic initiation factor 4A-III
  • Peptidylprolyl isomerase domain and WD repeat-containing protein 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • Protein CASC3
  • Protein FRG1
  • Protein mago nashi homolog
  • RNA helicase aquarius
  • RNA-binding protein 8A
  • SNW domain-containing protein 1
  • Serine/arginine repetitive matrix protein 2
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
  • UNK
  • WD repeat-containing protein 70
KeywordsSPLICING / spliceosome / RNA splicing / PRP16 / branching
Function / homology
Function and homology information


striated muscle dense body / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / post-spliceosomal complex / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / regulation of retinoic acid receptor signaling pathway ...striated muscle dense body / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / post-spliceosomal complex / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / intracellular mRNA localization / 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 / histone pre-mRNA 3'end processing complex / regulation of mRNA processing / negative regulation of excitatory postsynaptic potential / regulation of vitamin D receptor signaling pathway / 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 / nuclear retinoic acid receptor binding / embryonic brain development / oocyte development / embryonic cranial skeleton morphogenesis / protein methylation / alternative mRNA splicing, via spliceosome / U12-type spliceosomal complex / poly(A) binding / 7-methylguanosine cap hypermethylation / M-decay: degradation of maternal mRNAs by maternally stored factors / U1 snRNP binding / U2-type catalytic step 1 spliceosome / C2H2 zinc finger domain binding / RNA splicing, via transesterification reactions / methylosome / pre-mRNA binding / pICln-Sm protein complex / regulation of mRNA splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / mRNA 3'-end processing / snRNP binding / sno(s)RNA-containing ribonucleoprotein complex / small nuclear ribonucleoprotein complex / Notch binding / host-mediated activation of viral transcription / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / P granule / positive regulation of vitamin D receptor signaling pathway / telomerase holoenzyme complex / commitment complex / telomerase RNA binding / nuclear vitamin D receptor binding / U2-type prespliceosome assembly / U2-type spliceosomal complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / U2-type catalytic step 2 spliceosome / NOTCH4 Intracellular Domain Regulates Transcription / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / U4 snRNP / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / U2-type prespliceosome / inner cell mass cell proliferation / protein peptidyl-prolyl isomerization / ubiquitin-ubiquitin ligase activity / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / cyclosporin A binding / WD40-repeat domain binding / muscle organ development / precatalytic spliceosome / generation of catalytic spliceosome for second transesterification step / Notch-HLH transcription pathway / lipid biosynthetic process / regulation of alternative mRNA splicing, via spliceosome / Formation of paraxial mesoderm / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / mitotic G2 DNA damage checkpoint signaling / spliceosomal complex assembly / mRNA 3'-splice site recognition / exploration behavior / mRNA Splicing - Minor Pathway / negative regulation of DNA damage response, signal transduction by p53 class mediator
Similarity search - Function
Corepressor interacting with RBPJ 1 / : / 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 ...Corepressor interacting with RBPJ 1 / : / 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 / Protein CASC3 / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / Splicing factor Yju2 / Saf4/Yju2 protein / Saf4/Yju2 protein / 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 / Actin-crosslinking / : / 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 / mRNA splicing factor SYF2 / SYF2 splicing factor / Helix hairpin bin domain superfamily / : / : / 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 / : / G10 protein / Pre-mRNA-splicing factor BUD31 / 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. / DNA2/NAM7-like helicase / : / MIF4G domain / Small ribonucleoprotein associated, SmB/SmN / Myb-like DNA-binding domain / U2 small nuclear ribonucleoprotein A' / 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 / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Brr2, N-terminal helicase PWI domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / Protein CASC3 / Pleiotropic regulator 1 / RNA helicase aquarius ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / Protein CASC3 / 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 / 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 FRG1 / 116 kDa U5 small nuclear ribonucleoprotein component / Pre-mRNA-processing-splicing factor 8 / Corepressor interacting with RBPJ 1 / 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 / Splicing factor YJU2 / Crooked neck-like protein 1 / Pre-mRNA-splicing factor CWC22 homolog / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / 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)
unidentified adenovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhan, X. / Lu, Y. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Molecular basis for the activation of human spliceosome.
Authors: Xiechao Zhan / Yichen Lu / Yigong Shi /
Abstract: The spliceosome executes pre-mRNA splicing through four sequential stages: assembly, activation, catalysis, and disassembly. Activation of the spliceosome, namely remodeling of the pre-catalytic ...The spliceosome executes pre-mRNA splicing through four sequential stages: assembly, activation, catalysis, and disassembly. Activation of the spliceosome, namely remodeling of the pre-catalytic spliceosome (B complex) into the activated spliceosome (B complex) and the catalytically activated spliceosome (B complex), involves major flux of protein components and structural rearrangements. Relying on a splicing inhibitor, we have captured six intermediate states between the B and B complexes: pre-B, B-I, B-II, B-III, B-IV, and post-B. Their cryo-EM structures, together with an improved structure of the catalytic step I spliceosome (C complex), reveal how the catalytic center matures around the internal stem loop of U6 snRNA, how the branch site approaches 5'-splice site, how the RNA helicase PRP2 rearranges to bind pre-mRNA, and how U2 snRNP undergoes remarkable movement to facilitate activation. We identify a previously unrecognized key role of PRP2 in spliceosome activation. Our study recapitulates a molecular choreography of the human spliceosome during its catalytic activation.
History
DepositionJan 11, 2023Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
F: U6 snRNA
G: pre-mRNA
6: pre-mRNA
H: U2 snRNA
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
R: SNW domain-containing protein 1
S: Peptidyl-prolyl cis-trans isomerase-like 1
T: Pleiotropic regulator 1
Q: RNA helicase aquarius
U: Serine/arginine repetitive matrix protein 2
V: Pre-mRNA-splicing factor CWC22 homolog
W: Pre-mRNA-processing factor 17
X: Pre-mRNA-splicing factor CWC25 homolog
Y: Coiled-coil domain-containing protein 94
Z: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
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: Eukaryotic initiation factor 4A-III
v: Protein mago nashi homolog
w: RNA-binding protein 8A
x: Protein CASC3
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
o: U2 small nuclear ribonucleoprotein A'
p: U2 small nuclear ribonucleoprotein B''
y: Peptidyl-prolyl cis-trans isomerase E
z: Pre-mRNA-splicing factor ISY1 homolog
3: Peptidylprolyl isomerase domain and WD repeat-containing protein 1
4: Corepressor interacting with RBPJ 1
1: WD repeat-containing protein 70
2: Protein FRG1
5: UNK
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 F
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein G
g: Small nuclear ribonucleoprotein Sm D3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,241,20872
Polymers3,239,44558
Non-polymers1,76314
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 20 types, 21 molecules ACJLNPRTQUYuvwxia3412

#1: Protein Pre-mRNA-processing-splicing factor 8 / PRP8 homolog / Splicing factor Prp8


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 / SNU114 homolog / hSNU114


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 Crooked neck-like protein 1 / SYF3 / 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
#13: 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
#15: Protein Protein BUD31 homolog / 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
#17: 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
#18: 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
#20: 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 RNA helicase aquarius


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
#22: Protein Serine/arginine repetitive matrix protein 2 / Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa / Ser/Arg-related ...Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa / Ser/Arg-related nuclear matrix protein of 300 kDa


Mass: 300255.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35
#26: Protein Coiled-coil domain-containing protein 94


Mass: 37141.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BW85
#29: Protein Eukaryotic initiation factor 4A-III / eIF4A-III / ATP-dependent RNA helicase eIF4A-3 / Eukaryotic initiation factor 4A-like NUK-34 / ...eIF4A-III / ATP-dependent RNA helicase eIF4A-3 / Eukaryotic initiation factor 4A-like NUK-34 / Eukaryotic translation initiation factor 4A isoform 3


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
#30: 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
#31: Protein RNA-binding protein 8A / RNA-binding motif protein 8A / 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
#32: Protein Protein CASC3 / Cancer susceptibility candidate gene 3 protein


Mass: 76381.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15234
#34: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / SmB / 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
#44: 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
#45: Protein Corepressor interacting with RBPJ 1 / CBF1-interacting corepressor


Mass: 52441.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86X95
#46: 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
#47: 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

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RNA chain , 5 types, 5 molecules BFG6H

#2: 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 U6 snRNA


Mass: 34404.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#7: RNA chain pre-mRNA


Mass: 14729.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unidentified adenovirus
#8: RNA chain pre-mRNA


Mass: 55660.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unidentified adenovirus
#9: 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: 340097

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

#4: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / BRR2 / BRR2 homolog


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 / SNR40 / U5-40K / U5 snRNP-specific 40 kDa protein


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 ... , 8 types, 8 molecules IKMOVXZz

#10: Protein Pre-mRNA-splicing factor SYF1


Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7
#12: Protein Pre-mRNA-splicing factor SPF27 / 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
#14: 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
#16: Protein Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22


Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64
#23: Protein Pre-mRNA-splicing factor CWC22 homolog


Mass: 105646.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8
#25: Protein Pre-mRNA-splicing factor CWC25 homolog / Coiled-coil domain-containing protein 49


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


Mass: 140720.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92620, RNA helicase
#43: 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

#19: 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
#42: Protein Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / 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

#24: Protein Pre-mRNA-processing factor 17 / 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
#28: Protein
Pre-mRNA-processing factor 19 / 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, 12 molecules hgjbkcmdlenf

#33: Protein Small nuclear ribonucleoprotein Sm D3 / SmD3 / 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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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U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op

#40: Protein U2 small nuclear ribonucleoprotein A' / U2-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
#41: Protein U2 small nuclear ribonucleoprotein B'' / U2-B" / U2 / 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

+
Protein/peptide , 1 types, 1 molecules 5

#48: Protein/peptide UNK


Mass: 3178.905 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

+
Non-polymers , 4 types, 14 molecules

#49: 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
#50: 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
#51: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#52: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / 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: The human Bact-III complex / Type: COMPLEX / Entity ID: #1-#6, #9-#29, #32, #31, #30 / 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18223 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.012110798
ELECTRON MICROSCOPYf_angle_d1.206150686
ELECTRON MICROSCOPYf_dihedral_angle_d15.31221077
ELECTRON MICROSCOPYf_chiral_restr0.06415546
ELECTRON MICROSCOPYf_plane_restr0.00719468

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