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

Basic information

• Entry: Database: EMDB / ID: 9646
• Title: Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1 complex) at 2.9 angstrom resolution
• Map data: The 2.9 angstrom map of the human ILS1 complex

Sample

Human 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 / homology: 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
• Source: Homo sapiens (human) / Human (human)
• Method: single particle reconstruction / cryo EM / 2.9 Å resolution
• Authors: Zhang X / Zhan X / Yan C / Shi Y
• Citation: Journal: 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: PDB-ID: 6id0; ; SummaryFull reportAbout validation report
• Date: Deposition: Sep 7, 2018 / Header (metadata) release: Mar 13, 2019 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019

Map

• File: emd_9646.map.gz (map file in CCP4 format, 256001 KB)
• Voxel size: X=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 Number	1
Map Geometry	Axis order X Y Z Dimensions 400 400 400 Origin 0.0 0.0 0.0 Limit 399.0 399.0 399.0 Spacing 400 400 400
Cell	A=B=C: 535.2 Å α=β=γ: 90.0 deg.

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.338	1.338	1.338
M x/y/z	400	400	400
origin x/y/z	0.000	0.000	0.000
length x/y/z	535.200	535.200	535.200
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	400	400	400
D min/max/mean	-0.239	0.543	0.000

Supplemental data

Sample components

Entire Human Intron Lariat Spliceosome

• Entire: Name: Human Intron Lariat Spliceosome / Number of components: 37

Component #1: protein, Human Intron Lariat Spliceosome

• Protein: Name: Human Intron Lariat Spliceosome / Recombinant expression: No
• Source: Species: Homo sapiens (human)

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

• Protein: Name: Pre-mRNA-processing-splicing factor 8 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 273.97425 kDa
• Source: Species: Human (human)

Component #3: nucleic-acid, U5snRNA

Nucleic-acid

Name: U5snRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

AUACUCUGGU UUCUCUUCAG AUCGCAUAAA UCUUUCGCCU UUUACUAAAG AUUUCCGUGG AGAGGAACAA CUCUGAGUCU UAACCCAAUU UUUUGAGGCC UUGCUUUGGC AAGGCUA

• Mass: Theoretical: 37.254855 kDa
• Source: Species: Human (human)

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

• Protein: Name: 116 kDa U5 small nuclear ribonucleoprotein component / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 109.560625 kDa
• Source: Species: Human (human)

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

• Protein: Name: U5 small nuclear ribonucleoprotein 40 kDa protein / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 39.359492 kDa
• Source: Species: Human (human)

Component #6: nucleic-acid, U6snRNA

Nucleic-acid

Name: U6snRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

GUGCUCGCUU CGGCAGCACA UAUACUAAAA UUGGAACGAU ACAGAGAAGA UUAGCAUGGC CCCUGCGCAA GGAUGACACG CAAAUUCGUG AAGCGUUCCA UAUUUUU

• Mass: Theoretical: 34.404438 kDa
• Source: Species: Human (human)

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

• Protein: Name: Crooked neck-like protein 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 100.610008 kDa
• Source: Species: Human (human)

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

• Protein: Name: Cell division cycle 5-like protein / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 92.406883 kDa
• Source: Species: Human (human)

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

• Protein: Name: Pre-mRNA-splicing factor SYF2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 28.780518 kDa
• Source: Species: Human (human)

Component #10: protein, Protein BUD31 homolog

• Protein: Name: Protein BUD31 homolog / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 17.03285 kDa
• Source: Species: Human (human)

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

• Protein: Name: Pre-mRNA-splicing factor RBM22 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 46.959555 kDa
• Source: Species: Human (human)

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

• Protein: Name: Spliceosome-associated protein CWC15 homolog / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 26.674447 kDa
• Source: Species: Human (human)

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

• Protein: Name: SNW domain-containing protein 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 61.770648 kDa
• Source: Species: Human (human)

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

• Protein: Name: Peptidyl-prolyl cis-trans isomerase-like 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 18.257805 kDa
• Source: Species: Human (human)

Component #15: protein, Pleiotropic regulator 1

• Protein: Name: Pleiotropic regulator 1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 57.280758 kDa
• Source: Species: Human (human)

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

• Protein: Name: Pre-mRNA-processing factor 17 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 65.61218 kDa
• Source: Species: Human (human)

Component #17: nucleic-acid, pre-mRNA

Nucleic-acid

Name: 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

• Mass: Theoretical: 87.186328 kDa
• Source: Species: Human (human)

Component #18: nucleic-acid, U2snRNA

Nucleic-acid

Name: 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

• Mass: Theoretical: 60.186445 kDa
• Source: Species: Human (human)

Component #19: protein, CWF19-like protein 2

• Protein: Name: CWF19-like protein 2 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 103.976492 kDa
• Source: Species: Human (human)

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

• Protein: Name: Pre-mRNA-splicing factor SYF1 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 100.148711 kDa
• Source: Species: Human (human)

Component #21: protein, Small nuclear ribonucleoprotein Sm D3

• Protein: Name: Small nuclear ribonucleoprotein Sm D3 / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 13.940308 kDa
• Source: Species: Human (human)

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

• Protein: Name: Small nuclear ribonucleoprotein-associated protein / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 23.686004 kDa
• Source: Species: Human (human)

Component #23: protein, Small nuclear ribonucleoprotein Sm D1

• Protein: Name: Small nuclear ribonucleoprotein Sm D1 / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 13.310653 kDa
• Source: Species: Human (human)

Component #24: protein, Small nuclear ribonucleoprotein Sm D2

• Protein: Name: Small nuclear ribonucleoprotein Sm D2 / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 13.551928 kDa
• Source: Species: Human (human)

Component #25: protein, Small nuclear ribonucleoprotein F

• Protein: Name: Small nuclear ribonucleoprotein F / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 9.734171 kDa
• Source: Species: Human (human)

Component #26: protein, Small nuclear ribonucleoprotein E

• Protein: Name: Small nuclear ribonucleoprotein E / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 10.817601 kDa
• Source: Species: Human (human)

Component #27: protein, Small nuclear ribonucleoprotein G

• Protein: Name: Small nuclear ribonucleoprotein G / Number of Copies: 2 / Recombinant expression: No
• Mass: Theoretical: 8.508084 kDa
• Source: Species: Human (human)

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

• Protein: Name: Pre-mRNA-processing factor 19 / Number of Copies: 4 / Recombinant expression: No
• Mass: Theoretical: 55.245547 kDa
• Source: Species: Human (human)

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

• Protein: Name: Pre-mRNA-splicing factor SPF27 / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 26.16342 kDa
• Source: Species: Human (human)

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

• Protein: Name: U2 small nuclear ribonucleoprotein A' / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 28.456584 kDa
• Source: Species: Human (human)

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

• Protein: Name: U2 small nuclear ribonucleoprotein B'' / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 25.524367 kDa
• Source: Species: Human (human)

Component #32: protein, RNA helicase aquarius

• Protein: Name: RNA helicase aquarius / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 171.502453 kDa
• Source: Species: Human (human)

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

• Protein: Name: Peptidyl-prolyl cis-trans isomerase E / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 33.475773 kDa
• Source: Species: Human (human)

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

• Ligand: Name: INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 0.660035 kDa

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

• Ligand: Name: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
• Mass: Theoretical: 0.52318 kDa

Component #36: ligand, MAGNESIUM ION

• Ligand: Name: MAGNESIUM ION / Number of Copies: 7 / Recombinant expression: No
• Mass: Theoretical: 2.430505 MDa

Component #37: ligand, ZINC ION

• Ligand: Name: ZINC ION / Number of Copies: 7 / Recombinant expression: No
• Mass: Theoretical: 6.540905 MDa

Experimental details

Sample preparation

• Specimen: Specimen state: particle / Method: cryo EM
• Sample solution: pH: 7.9
• Vitrification: Cryogen name: ETHANE

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Imaging: Microscope: FEI TITAN KRIOS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Ų / Illumination mode: FLOOD BEAM
• Lens: Imaging mode: BRIGHT FIELD
• Specimen Holder: Model: OTHER
• Camera: Detector: GATAN K2 SUMMIT (4k x 4k)

Image processing

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

Atomic model buiding

Output model

6id0