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

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Entry
Database: PDB / ID: 8qoz
TitleCryo-EM Structure of Pre-B+5'ss+ATPgammaS Complex (core part)
Components
  • (U4/U6 small nuclear ribonucleoprotein ...) x 3
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • 5'ss RNA oligo
  • NHP2-like protein 1, N-terminally processed
  • Pre-mRNA-processing factor 6
  • Pre-mRNA-processing-splicing factor 8
  • Probable ATP-dependent RNA helicase DDX23
  • Splicing factor 3A subunit 1
  • Thioredoxin-like protein 4A
  • U4 snRNAU4 spliceosomal RNA
  • U4/U6.U5 tri-snRNP-associated protein 1
  • U5 small nuclear ribonucleoprotein 200 kDa helicase
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
  • Ubiquitin carboxyl-terminal hydrolase 39
KeywordsSPLICING / spliceosome
Function / homology
Function and homology information


spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / R-loop processing / U4atac snRNA binding / box C/D sno(s)RNA binding / snRNP binding ...spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / R-loop processing / U4atac snRNA binding / box C/D sno(s)RNA binding / snRNP binding / dense fibrillar component / cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D methylation guide snoRNP complex / U4/U6 snRNP / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / spliceosomal tri-snRNP complex / U4 snRNA binding / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / box C/D snoRNP assembly / U4 snRNP / rRNA modification in the nucleus and cytosol / U2 snRNP / U3 snoRNA binding / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / single fertilization / mRNA 3'-splice site recognition / MLL1 complex / spliceosomal tri-snRNP complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / RNA processing / U2 snRNA binding / Cajal body / U6 snRNA binding / spliceosomal snRNP assembly / ribonucleoprotein complex binding / pre-mRNA intronic binding / U1 snRNA binding / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / maturation of LSU-rRNA / catalytic step 2 spliceosome / small-subunit processome / mRNA Splicing - Major Pathway / RNA splicing / response to cocaine / helicase activity / spliceosomal complex / ribosomal small subunit biogenesis / mRNA processing / mRNA splicing, via spliceosome / osteoblast differentiation / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / ATPase binding / cytosolic large ribosomal subunit / cellular response to lipopolysaccharide / ubiquitinyl hydrolase 1 / RNA helicase activity / hydrolase activity / RNA helicase / nuclear speck / cell cycle / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin / nucleolus / GTP binding / Golgi apparatus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
USP39 / PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / PWI domain superfamily / PWI domain / PWI domain profile. ...USP39 / PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / PWI domain superfamily / PWI domain / PWI domain profile. / Pre-mRNA processing factor 4 (PRP4)-like / Splicing factor 3A subunit 1, ubiquitin domain / Splicing Factor Motif, present in Prp18 and Pr04 / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / pre-mRNA processing factor 3 domain / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / PWI domain / PWI, domain in splicing factors / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA splicing factor PRP21 like protein / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / H/ACA ribonucleoprotein complex, subunit Nhp2-like / Pre-mRNA-splicing factor Syf1-like / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / NOSIC / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Sec63 Brl domain / Snu114, GTP-binding domain / Tetratricopeptide repeat / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Sec63 domain / Sec63 Brl domain / HAT (Half-A-TPR) repeat / Tetratricopeptide repeat / HAT (Half-A-TPR) repeats / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / Elongation Factor G, domain II / Elongation Factor G, domain III / DEAD-box RNA helicase Q motif profile. / 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
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6.U5 tri-snRNP-associated protein 1 / U4/U6 small nuclear ribonucleoprotein Prp3 ...INOSITOL HEXAKISPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6.U5 tri-snRNP-associated protein 1 / U4/U6 small nuclear ribonucleoprotein Prp3 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / NHP2-like protein 1 / 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 small nuclear ribonucleoprotein Prp31 / Probable ATP-dependent RNA helicase DDX23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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: Zhang, Z. / Kumar, V. / Dybkov, O. / Will, C.L. / Zhong, J. / Ludwig, S. / Urlaub, H. / Kastner, B. / Stark, H. / Luehrmann, R.
History
DepositionSep 29, 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

Downloads & links

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Assembly

Deposited unit
B: U5 small nuclear ribonucleoprotein 200 kDa helicase
G: Probable ATP-dependent RNA helicase DDX23
J: U4/U6 small nuclear ribonucleoprotein Prp3
L: U4/U6 small nuclear ribonucleoprotein Prp31
F: U4/U6 small nuclear ribonucleoprotein Prp4
N: Pre-mRNA-processing factor 6
A: Pre-mRNA-processing-splicing factor 8
U: Ubiquitin carboxyl-terminal hydrolase 39
S: U4/U6.U5 tri-snRNP-associated protein 1
C: 116 kDa U5 small nuclear ribonucleoprotein component
M: NHP2-like protein 1, N-terminally processed
D: Thioredoxin-like protein 4A
5: U5 snRNA
z: 5'ss RNA oligo
7: Splicing factor 3A subunit 1
4: U4 snRNA
6: U6 snRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,194,30918
Polymers1,193,64917
Non-polymers6601
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 10 types, 10 molecules BGNAUSCMD7

#1: 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: 18527.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase
#2: 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
#6: 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
#7: 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
#8: Protein Ubiquitin carboxyl-terminal hydrolase 39 / SAD1 homolog / U4/U6.U5 tri-snRNP-associated 65 kDa protein


Mass: 65481.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q53GS9, ubiquitinyl hydrolase 1
#9: 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
#10: 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 NHP2-like protein 1, N-terminally processed


Mass: 14191.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55769
#12: 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
#15: 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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U4/U6 small nuclear ribonucleoprotein ... , 3 types, 3 molecules JLF

#3: Protein U4/U6 small nuclear ribonucleoprotein Prp3 / Pre-mRNA-splicing factor 3 / hPrp3 / U4/U6 snRNP 90 kDa protein


Mass: 77669.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43395
#4: 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
#5: Protein U4/U6 small nuclear ribonucleoprotein Prp4 / PRP4 homolog / hPrp4 / U4/U6 snRNP 60 kDa protein / WD splicing factor Prp4


Mass: 58536.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43172

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RNA chain , 4 types, 4 molecules 5z46

#13: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981
#14: RNA chain 5'ss RNA oligo


Mass: 3555.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#16: RNA chain U4 snRNA / U4 spliceosomal RNA


Mass: 46181.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 340142
#17: RNA chain U6 snRNA / U6 spliceosomal RNA


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

#18: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


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

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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+ATPyS complex / Type: COMPLEX / Entity ID: #1-#17 / 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 FIELDBright-field microscopy / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 411185 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00446700
ELECTRON MICROSCOPYf_angle_d0.52264124
ELECTRON MICROSCOPYf_dihedral_angle_d11.3578221
ELECTRON MICROSCOPYf_chiral_restr0.0397111
ELECTRON MICROSCOPYf_plane_restr0.0047524

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