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- EMDB-9646: Cryo-EM structure of a human intron lariat spliceosome prior to P... -

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Entry
Database: EMDB / ID: 9646
TitleCryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1 complex) at 2.9 angstrom resolution
Map dataThe 2.9 angstrom map of the human ILS1 complex
SampleHuman Intron Lariat Spliceosome
  • Pre-mRNA-processing-splicing factor 8
  • (nucleic-acidNucleic acid) x 4
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • U5 small nuclear ribonucleoprotein 40 kDa protein
  • Crooked neck-like protein 1
  • Cell division cycle 5-like protein
  • (Pre-mRNA-splicing factor ...) x 4
  • Protein BUD31 homolog
  • Spliceosome-associated protein CWC15 homolog
  • SNW domain-containing protein 1
  • (Peptidyl-prolyl cis-trans ...) x 2
  • Pleiotropic regulator 1
  • (Pre-mRNA-processing factor ...) x 2
  • CWF19-like protein 2
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • Small nuclear ribonucleoprotein-associated protein
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • RNA helicase aquarius
  • (ligand) x 4
Function / homologyHAT (Half-A-TPR) repeat / pre-mRNA splicing factor component / 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 / Tetratricopeptide repeat ...HAT (Half-A-TPR) repeat / pre-mRNA splicing factor component / 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 / Tetratricopeptide repeat / PROCT domain / RNA recognition motif of the spliceosomal PrP8 / Nucleotide-binding alpha-beta plait domain superfamily / PROCN domain / PRO8NT domain / U5-snRNA binding site 2 of PrP8 / Ribonuclease H-like superfamily / PRP8 domain IV core / Peptidyl-prolyl cis-trans isomerase E / LSM domain superfamily / Trp-Asp (WD) repeats signature. / Tetratricopeptide repeat / RNA recognition motif, spliceosomal PrP8 / Trp-Asp (WD) repeats profile. / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / G10 protein signature 2. / G10 protein signature 1. / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Sm-like protein Lsm6/SmF / Intron-binding protein aquarius N-terminus / BUD31/G10-related, conserved site / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / WD40-repeat-containing domain / Myb domain / SKI-interacting protein, SKIP / Small ribonucleoprotein associated, SmB/SmN / Tetratricopeptide-like helical domain superfamily / Homeobox-like domain superfamily / G-protein beta WD-40 repeat / Elongation factor EFG, domain V-like / PRO8NT (NUC069), PrP8 N-terminal domain / Leucine-rich repeat / LSM domain, eukaryotic/archaea-type / SANT/Myb domain / Transcription factor, GTP-binding domain / Breast carcinoma amplified sequence 2 (BCAS2) / Ricin B, lectin domain / Zinc finger, CCCH-type / G10 protein / JAB1/MPN/MOV34 metalloenzyme domain / Cwf15/Cwc15 cell cycle control protein / RNA recognition motif domain / Elongation factor Tu domain 2 / Elongation factor G, domain IV / U-box domain / Protein similar to CwfJ C-terminus 2 / WD40 repeat / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / U6-snRNA interacting domain of PrP8 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Pre-mRNA-splicing factor SPF27 / Pre-mRNA-splicing factor Cwf15/Cwc15 / Prp19/Pso4-like / Cwf19-like, C-terminal domain-1 / Cwf19-like protein, C-terminal domain-2 / Translation elongation factor EFG/EF2, domain IV / Translation elongation factor EFTu-like, domain 2 / SKIP/SNW domain / SKI-interacting protein SKIP, SNW domain / SYF2 splicing factor / PROCT (NUC072) domain / U box domain / U2A'/phosphoprotein 32 family A, C-terminal / HAT (Half-A-TPR) repeat / PROCN (NUC071) domain / WD40 repeat, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Ribosomal protein S5 domain 2-type fold / RNA-binding domain superfamily / WD40-repeat-containing domain superfamily / mRNA Splicing - Major Pathway / Neutrophil degranulation / HIT-like superfamily / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Zinc finger, CCCH-type superfamily / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Formation of TC-NER Pre-Incision Complex / EF-G domain III/V-like / Notch-HLH transcription pathway / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / NOTCH1 Intracellular Domain Regulates Transcription / mRNA Splicing - Minor Pathway / mRNA 3'-end processing / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / WD domain, G-beta repeat
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle 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 ReportPDB-ID: 6id0

SummaryFull reportAbout validation report
DateDeposition: Sep 7, 2018 / Header (metadata) release: Mar 13, 2019 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6id0
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9646.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.34 Å/pix.
= 535.2 Å
400 pix
1.34 Å/pix.
= 535.2 Å
400 pix
1.34 Å/pix.
= 535.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.338 Å
Density
Contour Level:0.025 (by author), 0.025 (movie #1):
Minimum - Maximum-0.23935571 - 0.5426388
Average (Standard dev.)0.00016763175 (0.0089349225)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 535.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3381.3381.338
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z535.200535.200535.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2390.5430.000

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Supplemental data

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Sample components

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Entire Human Intron Lariat Spliceosome

EntireName: Human Intron Lariat Spliceosome / Number of components: 37

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Component #1: protein, Human Intron Lariat Spliceosome

ProteinName: Human Intron Lariat Spliceosome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Pre-mRNA-processing-splicing factor 8

ProteinName: Pre-mRNA-processing-splicing factor 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 273.97425 kDa
SourceSpecies: Human (human)

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Component #3: nucleic-acid, U5snRNA

Nucleic-acidName: U5snRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUACUCUGGU UUCUCUUCAG AUCGCAUAAA UCUUUCGCCU UUUACUAAAG AUUUCCGUGG AGAGGAACAA CUCUGAGUCU UAACCCAAUU UUUUGAGGCC UUGCUUUGGC AAGGCUA
MassTheoretical: 37.254855 kDa
SourceSpecies: Human (human)

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Component #4: protein, 116 kDa U5 small nuclear ribonucleoprotein component

ProteinName: 116 kDa U5 small nuclear ribonucleoprotein component / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 109.560625 kDa
SourceSpecies: Human (human)

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Component #5: protein, U5 small nuclear ribonucleoprotein 40 kDa protein

ProteinName: U5 small nuclear ribonucleoprotein 40 kDa protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.359492 kDa
SourceSpecies: Human (human)

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Component #6: nucleic-acid, U6snRNA

Nucleic-acidName: U6snRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUGCUCGCUU CGGCAGCACA UAUACUAAAA UUGGAACGAU ACAGAGAAGA UUAGCAUGGC CCCUGCGCAA GGAUGACACG CAAAUUCGUG AAGCGUUCCA UAUUUUU
MassTheoretical: 34.404438 kDa
SourceSpecies: Human (human)

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Component #7: protein, Crooked neck-like protein 1

ProteinName: Crooked neck-like protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.610008 kDa
SourceSpecies: Human (human)

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Component #8: protein, Cell division cycle 5-like protein

ProteinName: Cell division cycle 5-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 92.406883 kDa
SourceSpecies: Human (human)

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Component #9: protein, Pre-mRNA-splicing factor SYF2

ProteinName: Pre-mRNA-splicing factor SYF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.780518 kDa
SourceSpecies: Human (human)

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Component #10: protein, Protein BUD31 homolog

ProteinName: Protein BUD31 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.03285 kDa
SourceSpecies: Human (human)

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Component #11: protein, Pre-mRNA-splicing factor RBM22

ProteinName: Pre-mRNA-splicing factor RBM22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.959555 kDa
SourceSpecies: Human (human)

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Component #12: protein, Spliceosome-associated protein CWC15 homolog

ProteinName: Spliceosome-associated protein CWC15 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.674447 kDa
SourceSpecies: Human (human)

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Component #13: protein, SNW domain-containing protein 1

ProteinName: SNW domain-containing protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 61.770648 kDa
SourceSpecies: Human (human)

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Component #14: protein, Peptidyl-prolyl cis-trans isomerase-like 1

ProteinName: Peptidyl-prolyl cis-trans isomerase-like 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.257805 kDa
SourceSpecies: Human (human)

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Component #15: protein, Pleiotropic regulator 1

ProteinName: Pleiotropic regulator 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.280758 kDa
SourceSpecies: Human (human)

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Component #16: protein, Pre-mRNA-processing factor 17

ProteinName: Pre-mRNA-processing factor 17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.61218 kDa
SourceSpecies: Human (human)

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Component #17: nucleic-acid, pre-mRNA

Nucleic-acidName: pre-mRNAPrimary transcript / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GAAUACACGG AAUUCGAGCU CGCCCACUCU UGGAUCGGAA ACCCGUCGGC CUCCGAACGG UAAGAGCCUA GCAUGUAGAA CUGGUUACCU GCAGCCCAAG CUUGCGUACA CCAUCAGGGU ACGUACUAGU ACGUACACCA UCAGGGUACG GCUGCACGUC UAGGGCGCAG UAGUCCAGGG UUUCCUUGAU GAUGUCAUAC UUAUCCUGUC CCUUUUUUUU CCACAGCUCG CGGUUGAGGA CAAACUCUUC GCGGUCUUUC CAGUGGGGAU CC
MassTheoretical: 87.186328 kDa
SourceSpecies: Human (human)

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Component #18: nucleic-acid, U2snRNA

Nucleic-acidName: U2snRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUCGCUUCUC GGCCUUUUGG CUAAGAUCAA GUGUAGUAUC UGUUCUUAUC AGUUUAAUAU CUGAUACGUC CUCUAUCCGA GGACAAUAUA UUAAAUGGAU UUUUGGAGCA GGGAGAUGGA AUAGGAGCUU GCUCCGUCCA CUCCACGCAU CGACCUGGUA UUGCAGUACC UCCAGGAACG GUGCACCC
MassTheoretical: 60.186445 kDa
SourceSpecies: Human (human)

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Component #19: protein, CWF19-like protein 2

ProteinName: CWF19-like protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 103.976492 kDa
SourceSpecies: Human (human)

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Component #20: protein, Pre-mRNA-splicing factor SYF1

ProteinName: Pre-mRNA-splicing factor SYF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.148711 kDa
SourceSpecies: Human (human)

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Component #21: protein, Small nuclear ribonucleoprotein Sm D3

ProteinName: Small nuclear ribonucleoprotein Sm D3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.940308 kDa
SourceSpecies: Human (human)

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Component #22: protein, Small nuclear ribonucleoprotein-associated protein

ProteinName: Small nuclear ribonucleoprotein-associated protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.686004 kDa
SourceSpecies: Human (human)

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Component #23: protein, Small nuclear ribonucleoprotein Sm D1

ProteinName: Small nuclear ribonucleoprotein Sm D1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.310653 kDa
SourceSpecies: Human (human)

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Component #24: protein, Small nuclear ribonucleoprotein Sm D2

ProteinName: Small nuclear ribonucleoprotein Sm D2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.551928 kDa
SourceSpecies: Human (human)

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Component #25: protein, Small nuclear ribonucleoprotein F

ProteinName: Small nuclear ribonucleoprotein F / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.734171 kDa
SourceSpecies: Human (human)

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Component #26: protein, Small nuclear ribonucleoprotein E

ProteinName: Small nuclear ribonucleoprotein E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.817601 kDa
SourceSpecies: Human (human)

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Component #27: protein, Small nuclear ribonucleoprotein G

ProteinName: Small nuclear ribonucleoprotein G / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.508084 kDa
SourceSpecies: Human (human)

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Component #28: protein, Pre-mRNA-processing factor 19

ProteinName: Pre-mRNA-processing factor 19 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 55.245547 kDa
SourceSpecies: Human (human)

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Component #29: protein, Pre-mRNA-splicing factor SPF27

ProteinName: Pre-mRNA-splicing factor SPF27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.16342 kDa
SourceSpecies: Human (human)

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Component #30: protein, U2 small nuclear ribonucleoprotein A'

ProteinName: U2 small nuclear ribonucleoprotein A' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.456584 kDa
SourceSpecies: Human (human)

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Component #31: protein, U2 small nuclear ribonucleoprotein B''

ProteinName: U2 small nuclear ribonucleoprotein B'' / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.524367 kDa
SourceSpecies: Human (human)

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Component #32: protein, RNA helicase aquarius

ProteinName: RNA helicase aquarius / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 171.502453 kDa
SourceSpecies: Human (human)

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Component #33: protein, Peptidyl-prolyl cis-trans isomerase E

ProteinName: Peptidyl-prolyl cis-trans isomerase E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.475773 kDa
SourceSpecies: Human (human)

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Component #34: ligand, INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE

LigandName: INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.660035 kDa

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Component #35: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #36: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #37: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 390072
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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