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- PDB-6id0: Cryo-EM structure of a human intron lariat spliceosome prior to P... -

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Entry
Database: PDB / ID: 6id0
TitleCryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1 complex) at 2.9 angstrom resolution
Components
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 4
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • CWF19-like protein 2
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • RNA helicase aquarius
  • SNW domain-containing protein 1
  • Small nuclear ribonucleoprotein-associated protein
  • Spliceosome-associated protein CWC15 homolog
  • U2snRNA
  • U5 small nuclear ribonucleoprotein 40 kDa protein
  • U5snRNA
  • U6snRNA
  • pre-mRNAPrimary transcript
KeywordsSPLICING / Human Intron Lariat Spliceosome
Function / homologyLeucine-rich repeat / G-protein beta WD-40 repeat / CWF11 family / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / PRP8 domain IV core / Pre-mRNA splicing factor component Cdc5p/Cef1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Ribosomal protein S5 domain 2-type fold / WD40 repeat, conserved site / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 ...Leucine-rich repeat / G-protein beta WD-40 repeat / CWF11 family / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / PRP8 domain IV core / Pre-mRNA splicing factor component Cdc5p/Cef1 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Ribosomal protein S5 domain 2-type fold / WD40 repeat, conserved site / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Tetratricopeptide repeat / RNA recognition motif, spliceosomal PrP8 / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / BUD31/G10-related, conserved site / WD40-repeat-containing domain / Myb domain / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein Sm D2 / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein F / RNA-binding domain superfamily / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / EF-G domain III/V-like / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Small nuclear ribonucleoprotein D1 / Small nuclear ribonucleoprotein Sm D3 / P-loop containing nucleoside triphosphate hydrolase / Small nuclear ribonucleoprotein G / Pre-mRNA-processing factor 17 / Leucine-rich repeat domain superfamily / Intron-binding protein aquarius, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / Cyclophilin-like domain superfamily / Pre-mRNA-processing-splicing factor 8 / SKI-interacting protein, SKIP / Sm-like protein Lsm6/SmF / WD40-repeat-containing domain superfamily / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Translation elongation factor EFG/EF2, domain IV / Small GTP-binding protein domain / Translation elongation factor EFTu-like, domain 2 / SKI-interacting protein SKIP, SNW domain / U box domain / U2A'/phosphoprotein 32 family A, C-terminal / HAT (Half-A-TPR) repeat / G10 protein / Cwf19-like, C-terminal domain-1 / WD40 repeat / Leucine-rich repeat / LSM domain, eukaryotic/archaea-type / SANT/Myb domain / Transcription factor, GTP-binding domain / Ricin B, lectin domain / Elongation factor EFG, domain V-like / Cwf19-like protein, C-terminal domain-2 / Pre-mRNA-splicing factor Cwf15/Cwc15 / Peptidyl-prolyl cis-trans isomerase E / PROCT domain / WD40/YVTN repeat-like-containing domain superfamily / Myb-like transcription factor / Ribosomal protein S5 domain 2-type fold, subgroup / Pre-mRNA-splicing factor 19 / mRNA splicing factor SYF2 / Zinc finger, RING/FYVE/PHD-type / Tetratricopeptide repeat-containing domain / Nucleotide-binding alpha-beta plait domain superfamily / Pre-mRNA-splicing factor SPF27 / PROCN domain / PRO8NT domain / Ribonuclease H-like superfamily / Tetratricopeptide-like helical domain superfamily / LSM domain superfamily / Homeobox-like domain superfamily / Translation protein, beta-barrel domain superfamily / HIT-like superfamily / Zinc finger, CCCH-type superfamily / RNA recognition motif domain / SLBP independent Processing of Histone Pre-mRNAs / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / NOTCH1 Intracellular Domain Regulates Transcription / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / snRNP Assembly / Pre-NOTCH Transcription and Translation / Transport of Mature mRNA derived from an Intron-Containing Transcript / Cleavage of Growing Transcript in the Termination Region / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / U-box domain profile. / Leucine-rich repeat profile. / Myb-type HTH DNA-binding domain profile. / Trp-Asp (WD) repeats circular profile. / MPN domain profile. / Zinc finger C3H1-type profile. / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Notch-HLH transcription pathway / Trp-Asp (WD) repeats profile. / RUNX3 regulates NOTCH signaling
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.9 Å resolution
AuthorsZhang, X. / Zhan, X. / Yan, C. / Shi, Y.
CitationJournal: Cell Res. / Year: 2019
Title: Structures of the human spliceosomes before and after release of the ligated exon.
Authors: Xiaofeng Zhang / Xiechao Zhan / Chuangye Yan / Wenyu Zhang / Dongliang Liu / Jianlin Lei / Yigong Shi
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 7, 2018 / Release: Mar 13, 2019

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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: U5snRNA
C: 116 kDa U5 small nuclear ribonucleoprotein component
E: U5 small nuclear ribonucleoprotein 40 kDa protein
F: U6snRNA
J: Crooked neck-like protein 1
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
W: Pre-mRNA-processing factor 17
G: pre-mRNA
H: U2snRNA
U: CWF19-like protein 2
I: Pre-mRNA-splicing factor SYF1
a: Small nuclear ribonucleoprotein Sm D3
b: Small nuclear ribonucleoprotein-associated protein
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
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
K: Pre-mRNA-splicing factor SPF27
h: Small nuclear ribonucleoprotein Sm D3
i: Small nuclear ribonucleoprotein-associated protein
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''
Q: RNA helicase aquarius
y: Peptidyl-prolyl cis-trans isomerase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,056,45158
Polyers2,054,64042
Non-polymers1,81116
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 12 types, 13 molecules ACEJLNPRTUbiQ

#1: Protein/peptide 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: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#3: Protein/peptide 116 kDa U5 small nuclear ribonucleoprotein component / 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: (natural) Homo sapiens (human) / References: UniProt: Q15029
#4: Protein/peptide U5 small nuclear ribonucleoprotein 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: (natural) Homo sapiens (human) / References: UniProt: Q96DI7
#6: Protein/peptide Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 100610.008 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0
#7: Protein/peptide Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#9: Protein/peptide Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#11: Protein/peptide Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013
#12: Protein/peptide 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: (natural) Homo sapiens (human) / References: UniProt: Q13573
#14: Protein/peptide Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#18: Protein/peptide CWF19-like protein 2


Mass: 103976.492 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q2TBE0
#21: Protein/peptide Small nuclear ribonucleoprotein-associated protein


Mass: 23686.004 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: Q66K91
#31: Protein/peptide RNA helicase aquarius / Intron-binding protein of 160 kDa / IBP160


Mass: 171502.453 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O60306, RNA helicase

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RNA chain , 4 types, 4 molecules BFGH

#2: RNA chain U5snRNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981
#5: RNA chain U6snRNA


Mass: 34404.438 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#16: RNA chain pre-mRNA / Primary transcript


Mass: 87186.328 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
#17: RNA chain U2snRNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: GenBank: 340097

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Pre-mRNA-splicing factor ... , 4 types, 4 molecules MOIK

#8: Protein/peptide Pre-mRNA-splicing factor SYF2 / CCNDBP1-interactor / p29


Mass: 28780.518 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O95926
#10: Protein/peptide Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


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


Mass: 100148.711 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7
#28: Protein/peptide Pre-mRNA-splicing factor SPF27 / 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: (natural) Homo sapiens (human) / References: UniProt: O75934

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

#13: Protein/peptide Peptidyl-prolyl cis-trans isomerase-like 1 / PPIase / Rotamase PPIL1


Mass: 18257.805 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase
#32: Protein/peptide Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E


Mass: 33475.773 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNP9, peptidylprolyl isomerase

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

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


Mass: 65612.180 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O60508
#27: Protein/peptide
Pre-mRNA-processing factor 19 / 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: (natural) Homo sapiens (human)
References: UniProt: Q9UMS4, RING-type E3 ubiquitin transferase

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

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


Mass: 13940.308 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#22: Protein/peptide Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#23: Protein/peptide Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#24: Protein/peptide Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#25: Protein/peptide Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#26: Protein/peptide Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


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

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U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op

#29: Protein/peptide U2 small nuclear ribonucleoprotein A' / U2 snRNP A'


Mass: 28456.584 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P09661
#30: Protein/peptide U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


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

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Non-polymers , 4 types, 16 molecules

#33: Chemical ChemComp-I6P / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Formula: C6H18O24P6 / Phytic acid
#34: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#35: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Formula: Mg / Magnesium
#36: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Formula: Zn / Zinc

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Human Intron Lariat Spliceosome / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32
Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 390072 / Symmetry type: POINT
Least-squares processHighest resolution: 2.9 Å

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