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- PDB-8qpk: Cryo-EM Structure of Pre-B+5'ss Complex (core part) -

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Basic information

Entry
Database: PDB / ID: 8qpk
TitleCryo-EM Structure of Pre-B+5'ss Complex (core part)
Components
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • 5'ss oligo
  • Pre-mRNA-processing factor 6
  • Pre-mRNA-processing-splicing factor 8
  • Probable ATP-dependent RNA helicase DDX23
  • RNA-binding protein 42
  • Splicing factor 3A subunit 1
  • Thioredoxin-like protein 4A
  • U4 snRNA
  • U4/U6 small nuclear ribonucleoprotein Prp31
  • U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein
  • U4/U6.U5 tri-snRNP-associated protein 1
  • U5 small nuclear ribonucleoprotein 200 kDa helicase
  • U5 snRNA
  • U6 snRNA
  • Ubiquitin carboxyl-terminal hydrolase 39
KeywordsSPLICING / spliceosome
Function / homology
Function and homology information


ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / R-loop processing / cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / RNA splicing, via transesterification reactions ...ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / R-loop processing / cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / snRNP binding / U4 snRNA binding / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / mRNA 3'-splice site recognition / negative regulation of mRNA splicing, via spliceosome / MLL1 complex / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / protein deubiquitination / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / ribonucleoprotein complex binding / U1 snRNA binding / Cajal body / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / response to cocaine / spliceosomal complex / helicase activity / mRNA splicing, via spliceosome / cellular response to xenobiotic stimulus / mRNA processing / osteoblast differentiation / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / protein-macromolecule adaptor activity / nucleic acid binding / ubiquitinyl hydrolase 1 / RNA helicase activity / hydrolase activity / nuclear speck / cilium / ciliary basal body / RNA helicase / cell division / intracellular membrane-bounded organelle / GTPase activity / mRNA binding / centrosome / chromatin / GTP binding / nucleolus / Golgi apparatus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
U4/U6.U5 small nuclear ribonucleoprotein 27kDa protein / RBM42, RNA recognition motif / U4/U6.U5 small nuclear ribonucleoproteins / : / USP39 / DDX23-like domain / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif ...U4/U6.U5 small nuclear ribonucleoprotein 27kDa protein / RBM42, RNA recognition motif / U4/U6.U5 small nuclear ribonucleoproteins / : / USP39 / DDX23-like domain / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Splicing factor 3A subunit 1, ubiquitin domain / Prp31 C terminal domain / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal / Splicing factor 3A subunit 1, conserved domain / Splicing factor 3A subunit 1 / Pre-mRNA splicing factor PRP21 like protein / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / : / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Tetratricopeptide repeat / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Pre-mRNA-splicing factor Syf1-like / Sec63 domain / Sec63 Brl domain / Tetratricopeptide repeat / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / DEAD-box subfamily ATP-dependent helicases signature. / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Elongation Factor G, domain II / Elongation Factor G, domain III / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / Translation elongation factor EFTu-like, domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Elongation factor Tu domain 2 / MPN domain / MPN domain profile. / Tetratricopeptide repeats
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / U4/U6.U5 tri-snRNP-associated protein 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 ...INOSITOL HEXAKISPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / U4/U6.U5 tri-snRNP-associated protein 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / Thioredoxin-like protein 4A / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3A subunit 1 / Ubiquitin carboxyl-terminal hydrolase 39 / Pre-mRNA-processing-splicing factor 8 / U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein / U4/U6 small nuclear ribonucleoprotein Prp31 / RNA-binding protein 42 / Probable ATP-dependent RNA helicase DDX23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsZhang, Z. / Kumar, V. / Dybkov, O. / Will, C.L. / Zhong, J. / Ludwig, S. / Urlaub, H. / Kastner, B. / Stark, H. / Luehrmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nature / Year: 2024
Title: Structural insights into the cross-exon to cross-intron spliceosome switch.
Authors: Zhenwei Zhang / Vinay Kumar / Olexandr Dybkov / Cindy L Will / Jiayun Zhong / Sebastian E J Ludwig / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann /
Abstract: Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron. Alternatively, it can occur ...Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron. Alternatively, it can occur through an exon-defined pathway, whereby U2 binds the branch site located upstream of the defined exon and U1 snRNP interacts with the 5' splice site located directly downstream of it. The U4/U6.U5 tri-snRNP subsequently binds to produce a cross-intron (CI) or cross-exon (CE) pre-B complex, which is then converted to the spliceosomal B complex. Exon definition promotes the splicing of upstream introns and plays a key part in alternative splicing regulation. However, the three-dimensional structure of exon-defined spliceosomal complexes and the molecular mechanism of the conversion from a CE-organized to a CI-organized spliceosome, a pre-requisite for splicing catalysis, remain poorly understood. Here cryo-electron microscopy analyses of human CE pre-B complex and B-like complexes reveal extensive structural similarities with their CI counterparts. The results indicate that the CE and CI spliceosome assembly pathways converge already at the pre-B stage. Add-back experiments using purified CE pre-B complexes, coupled with cryo-electron microscopy, elucidate the order of the extensive remodelling events that accompany the formation of B complexes and B-like complexes. The molecular triggers and roles of B-specific proteins in these rearrangements are also identified. We show that CE pre-B complexes can productively bind in trans to a U1 snRNP-bound 5' splice site. Together, our studies provide new mechanistic insights into the CE to CI switch during spliceosome assembly and its effect on pre-mRNA splice site pairing at this stage.
History
DepositionOct 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Probable ATP-dependent RNA helicase DDX23
D: Thioredoxin-like protein 4A
L: U4/U6 small nuclear ribonucleoprotein Prp31
A: Pre-mRNA-processing-splicing factor 8
R: RNA-binding protein 42
U: Ubiquitin carboxyl-terminal hydrolase 39
S: U4/U6.U5 tri-snRNP-associated protein 1
C: 116 kDa U5 small nuclear ribonucleoprotein component
5: U5 snRNA
4: U4 snRNA
X: U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein
z: 5'ss oligo
6: U6 snRNA
N: Pre-mRNA-processing factor 6
B: U5 small nuclear ribonucleoprotein 200 kDa helicase
7: Splicing factor 3A subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,339,60217
Polymers1,338,94216
Non-polymers6601
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area52290 Å2
ΔGint-388 kcal/mol
Surface area213520 Å2

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Components

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Protein , 12 types, 12 molecules GDLARUSCXNB7

#1: Protein Probable ATP-dependent RNA helicase DDX23


Mass: 95785.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BUQ8
#2: Protein Thioredoxin-like protein 4A / DIM1 protein homolog / Spliceosomal U5 snRNP-specific 15 kDa protein / Thioredoxin-like U5 snRNP ...DIM1 protein homolog / Spliceosomal U5 snRNP-specific 15 kDa protein / Thioredoxin-like U5 snRNP protein U5-15kD


Mass: 16807.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83876
#3: Protein U4/U6 small nuclear ribonucleoprotein Prp31 / Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP ...Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP 61 kDa protein / Protein 61K / hPrp31


Mass: 55528.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WWY3
#4: 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
#5: Protein RNA-binding protein 42 / RNA-binding motif protein 42


Mass: 50477.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BTD8
#6: Protein Ubiquitin carboxyl-terminal hydrolase 39


Mass: 65481.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q53GS9
#7: Protein U4/U6.U5 tri-snRNP-associated protein 1 / SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / SART-1 / hSART-1 ...SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / SART-1 / hSART-1 / U4/U6.U5 tri-snRNP-associated 110 kDa protein


Mass: 90414.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43290
#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 U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein / U4/U6.U5 snRNP 27 kDa protein / U4/U6.U5-27K / Nucleic acid-binding protein RY-1 / U4/U6.U5 tri- ...U4/U6.U5 snRNP 27 kDa protein / U4/U6.U5-27K / Nucleic acid-binding protein RY-1 / U4/U6.U5 tri-snRNP-associated 27 kDa protein / 27K / U4/U6.U5 tri-snRNP-associated protein 3


Mass: 18915.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WVK2
#14: Protein Pre-mRNA-processing factor 6 / Androgen receptor N-terminal domain-transactivating protein 1 / ANT-1 / PRP6 homolog / U5 snRNP- ...Androgen receptor N-terminal domain-transactivating protein 1 / ANT-1 / PRP6 homolog / U5 snRNP-associated 102 kDa protein / U5-102 kDa protein


Mass: 107092.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O94906
#15: 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
#16: Protein Splicing factor 3A subunit 1 / SF3a120 / Spliceosome-associated protein 114 / SAP 114


Mass: 88991.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15459

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RNA chain , 4 types, 4 molecules 54z6

#9: 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
#10: RNA chain U4 snRNA


Mass: 46181.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 340142
#12: RNA chain 5'ss oligo


Mass: 3555.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#13: RNA chain U6 snRNA


Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_004394.1

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Non-polymers , 1 types, 1 molecules

#17: 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

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Details

Has ligand of interestY
Has protein modificationN

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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 spliceosomal pre-B+5'ss complex / Type: COMPLEX / Entity ID: #1-#8, #11-#12, #14, #9-#10, #13, #15-#16 / Source: NATURAL
Molecular weightExperimental value: NO
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: 5000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176879 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00230544
ELECTRON MICROSCOPYf_angle_d0.45942973
ELECTRON MICROSCOPYf_dihedral_angle_d11.6596636
ELECTRON MICROSCOPYf_chiral_restr0.0375205
ELECTRON MICROSCOPYf_plane_restr0.0044989

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