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- PDB-9if7: Cryo-EM structure of the kinetoplastid trans-spliceosome activate... -

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Basic information

Entry
Database: PDB / ID: 9if7
TitleCryo-EM structure of the kinetoplastid trans-spliceosome activated for catalytic step II (C* complex)
Components
  • (Guanine nucleotide-binding protein subunit beta-like ...) x 3
  • (LSM domain-containing ...) x 2
  • (Pre-mRNA-splicing factor ...) x 5
  • (RRM domain-containing ...) x 2
  • (Sm domain-containing ...) x 3
  • (Small nuclear ...) x 6
  • ATP-dependent RNA helicase, putative
  • CWF21 domain-containing protein
  • Cell division control protein
  • Crooked neck-like protein 1
  • G10 protein
  • Lsm5p, putative
  • Lsm7p protein, putative
  • MI domain-containing protein
  • Mago nashi-like protein,putative
  • NF-kappa-B-activating protein C-terminal domain-containing protein
  • PRKR-interacting protein 1
  • PRP19-related complex protein 3
  • Pre-mRNA-processing factor 19
  • Probable RNA helicase
  • Probable eukaryotic initiation factor 4A
  • Prp8 protein homologue, putative
  • RNA helicase
  • RNA-binding motif protein
  • SL RNA exon
  • SL RNA outron
  • SNW domain-containing protein 1
  • Sm protein B
  • Sm protein F
  • Sm protein G
  • Spliceosome-associated CWC15-like protein
  • Splicing factor Cactin C-terminal domain-containing protein
  • Splicing regulator SDE2-like protein
  • U2 small nuclear ribonucleoprotein 40K, putative
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
  • U6 snRNA-associated Sm-like protein LSm4
  • Uncharacterized protein
  • Unidentified protein
  • Unspecified product
  • Y-branched pre-mRNA
  • Zinc knuckle
  • peptidylprolyl isomerase
KeywordsSPLICING / Trans-spliceosome / Spliceosome
Function / homology
Function and homology information


U2-type post-spliceosomal complex / spliceosomal complex disassembly / exon-exon junction complex / pre-mRNA 3'-splice site binding / Lsm1-7-Pat1 complex / U6 snRNP / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / U12-type spliceosomal complex / pICln-Sm protein complex ...U2-type post-spliceosomal complex / spliceosomal complex disassembly / exon-exon junction complex / pre-mRNA 3'-splice site binding / Lsm1-7-Pat1 complex / U6 snRNP / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / U12-type spliceosomal complex / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / U4 snRNP / snRNP binding / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / U1 snRNP / U2 snRNP / U2-type prespliceosome / generation of catalytic spliceosome for second transesterification step / precatalytic spliceosome / spliceosomal complex assembly / Prp19 complex / spliceosomal tri-snRNP complex assembly / U5 snRNP / U5 snRNA binding / pre-mRNA intronic binding / U2 snRNA binding / nuclear-transcribed mRNA catabolic process / U6 snRNA binding / U4/U6 x U5 tri-snRNP complex / U1 snRNA binding / RNA processing / protein K63-linked ubiquitination / spliceosomal snRNP assembly / catalytic step 2 spliceosome / spliceosomal complex / translation initiation factor activity / RNA splicing / helicase activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / RING-type E3 ubiquitin transferase / mRNA processing / metallopeptidase activity / regulation of gene expression / ubiquitin protein ligase activity / nucleic acid binding / RNA helicase activity / RNA helicase / ribosome / ribonucleoprotein complex / hydrolase activity / DNA repair / mRNA binding / chromatin binding / GTPase activity / GTP binding / DNA binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Zinc knuckle / NF-kappa-B-activating protein, C-terminal / NF-kappa-B-activating protein / NF-kappa-B-activating protein C-terminal domain / Cactin, C-terminal / Cactus-binding C-terminus of cactin protein / Prp18 / Pre-mRNA-splicing factor 18 / Prp18 domain / Pre-mRNA-splicing factor SLU7 ...Zinc knuckle / NF-kappa-B-activating protein, C-terminal / NF-kappa-B-activating protein / NF-kappa-B-activating protein C-terminal domain / Cactin, C-terminal / Cactus-binding C-terminus of cactin protein / Prp18 / Pre-mRNA-splicing factor 18 / Prp18 domain / Pre-mRNA-splicing factor SLU7 / Mago nashi protein / Mago nashi superfamily / Mago nashi protein / cwf21 / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / Sm-like protein Lsm4 / U6 snRNA-associated Sm-like protein Lsm1/8 / Helix hairpin bin domain superfamily / : / Cactus-binding C-terminus of cactin protein / mRNA splicing factor Cwf21 domain / Pre-mRNA-processing factor 17 / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / : / : / Prp19/Pso4-like / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Myb-like domain profile. / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / U-box domain / WD repeat Prp46/PLRG1-like / G10 protein / : / Pre-mRNA-splicing factor BUD31 / Initiation factor eIF-4 gamma, MA3 / : / : / MA3 domain / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / U2 small nuclear ribonucleoprotein A' / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Brr2, N-terminal helicase PWI domain / N-terminal helicase PWI domain / : / Winged Helix-turn-helix domain / Sec63 Brl domain / U-box domain profile. / Leucine-rich repeat / : / Pre-mRNA-splicing factor Syf1-like / Snu114, GTP-binding domain / Modified RING finger domain / U-box domain / Sec63 domain / Sec63 Brl domain / : / Nucleolar protein 10-like, N-terminal domain / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / Myb-type HTH DNA-binding domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / Myb domain / : / Sm domain profile. / DEAD-box RNA helicase Q motif profile. / Myb-like DNA-binding domain / Elongation Factor G, domain II / Elongation Factor G, domain III / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / LSM domain superfamily / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-G5J / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / : ...ADENOSINE-5'-DIPHOSPHATE / Chem-G5J / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / CWF21 domain-containing protein / Sm domain-containing protein / Sm domain-containing protein / Pre-mRNA-splicing factor SLU7 / G10 protein / Uncharacterized protein / Cell division control protein / ATP-dependent RNA helicase, putative / Uncharacterized protein / LSM domain-containing protein / Uncharacterized protein / Pre-mRNA-splicing factor 18 / Pre-mRNA-splicing factor Syf1-like N-terminal HAT-repeats domain-containing protein / Small nuclear ribonucleoprotein, putative / peptidylprolyl isomerase / Lsm7p protein, putative / Sm domain-containing protein / Guanine nucleotide-binding protein subunit beta-like protein / Guanine nucleotide-binding protein subunit beta-like protein / RRM domain-containing protein / Pre-mRNA-processing factor 19 / Small nuclear ribonucleoprotein E / Mago nashi-like protein,putative / U2 small nuclear ribonucleoprotein 40K, putative / Lsm5p, putative / RRM domain-containing protein / Uncharacterized protein / Sm protein G / U6 snRNA-associated Sm-like protein LSm4 / Sm protein B / Small nuclear ribonucleoprotein Sm D2 / LSM domain-containing protein / Small nuclear ribonucleoprotein component-like protein / Probable eukaryotic initiation factor 4A / Uncharacterized protein / Splicing factor Cactin C-terminal domain-containing protein / Zinc knuckle / Prp8 protein homologue, putative / Small nuclear ribonucleoprotein Sm D3 / Sm protein F / Pre-mRNA-splicing factor Syf1/CRNKL1-like C-terminal HAT-repeats domain-containing protein / RNA helicase / Nucleolar protein 10-like N-terminal domain-containing protein / Unspecified product / Uncharacterized protein / MI domain-containing protein / NF-kappa-B-activating protein C-terminal domain-containing protein / Small nuclear ribonucleaoprotein, putative
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsNadenoen, T. / Vanden Broeck, A.
Funding support Belgium, European Union, 2items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)MISU F.6005.25 Belgium
European Research Council (ERC)TranSplice 101162011European Union
CitationJournal: To Be Published
Title: Structural basis for kinetoplastid SL trans-splicing
Authors: Nadenoen, T. / Vanden Broeck, A.
History
DepositionFeb 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L7: Probable eukaryotic initiation factor 4A
L8: RRM domain-containing protein
L9: Mago nashi-like protein,putative
LA: Prp8 protein homologue, putative
LB: ATP-dependent RNA helicase, putative
LC: Small nuclear ribonucleoprotein component-like protein
LD: PRKR-interacting protein 1
LF: Splicing factor Cactin C-terminal domain-containing protein
LG: RNA-binding motif protein
LH: Splicing regulator SDE2-like protein
LJ: Guanine nucleotide-binding protein subunit beta-like protein
LL: G10 protein
LN: Guanine nucleotide-binding protein subunit beta-like protein
LP: Spliceosome-associated CWC15-like protein
LQ: Cell division control protein
LR: CWF21 domain-containing protein
LS: Crooked neck-like protein 1
LT: Pre-mRNA-splicing factor SYF1
LV: RNA helicase
LW: U2 small nuclear ribonucleoprotein 40K, putative
LY: RRM domain-containing protein
LZ: NF-kappa-B-activating protein C-terminal domain-containing protein
SA: MI domain-containing protein
SC: Pre-mRNA-splicing factor SLU7
SD: Pre-mRNA-splicing factor 18
SF: Uncharacterized protein
SJ: PRP19-related complex protein 3
SK: Unspecified product
SL: SNW domain-containing protein 1
SN: peptidylprolyl isomerase
SO: Guanine nucleotide-binding protein subunit beta-like protein
SP: Pre-mRNA-splicing factor ISY1 homolog
SQ: Zinc knuckle
SS: Pre-mRNA-splicing factor SPF27
ST: Pre-mRNA-processing factor 19
SU: Pre-mRNA-processing factor 19
SV: Pre-mRNA-processing factor 19
SW: Pre-mRNA-processing factor 19
TN: Probable RNA helicase
UX: Unidentified protein
62: LSM domain-containing protein
63: Sm domain-containing protein
64: U6 snRNA-associated Sm-like protein LSm4
65: LSM domain-containing protein
66: Sm domain-containing protein
67: Lsm7p protein, putative
68: Sm domain-containing protein
RN: Y-branched pre-mRNA
24: Small nuclear ribonucleoprotein, putative
25: Small nuclear ribonucleoprotein Sm D2
2C: Lsm5p, putative
2D: Small nuclear ribonucleaoprotein, putative
2H: Small nuclear ribonucleoprotein E
2I: Sm protein F
2J: Sm protein G
51: Small nuclear ribonucleoprotein, putative
52: Small nuclear ribonucleoprotein Sm D2
53: Small nuclear ribonucleoprotein Sm D3
5B: Sm protein B
5E: Small nuclear ribonucleoprotein E
5F: Sm protein F
5G: Sm protein G
LE: SL RNA exon
LO: SL RNA outron
N2: U2 snRNA
N5: U5 snRNA
N6: U6 snRNA
U1: Small nuclear ribonucleoprotein, putative
U2: Small nuclear ribonucleoprotein Sm D2
U3: Small nuclear ribonucleoprotein Sm D3
UB: Sm protein B
UE: Small nuclear ribonucleoprotein E
UF: Sm protein F
UG: Sm protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,816,28097
Polymers2,812,67274
Non-polymers3,60923
Water00
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 , 31 types, 39 molecules L7L9LALBLDLFLGLHLLLPLQLRLSLVLWLZSASFSJSKSLSNSQSTSUSVSWTN6467...

#1: Protein Probable eukaryotic initiation factor 4A / ATP-dependent RNA helicase eIF4A


Mass: 44002.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KRB9, RNA helicase
#3: Protein Mago nashi-like protein,putative


Mass: 18684.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KMM3
#4: Protein Prp8 protein homologue, putative


Mass: 278149.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KTJ2
#5: Protein ATP-dependent RNA helicase, putative


Mass: 261270.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KDJ4
#7: Protein PRKR-interacting protein 1


Mass: 18266.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KD47
#8: Protein Splicing factor Cactin C-terminal domain-containing protein


Mass: 78806.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KRR3
#9: Protein RNA-binding motif protein


Mass: 8723.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10
#10: Protein Splicing regulator SDE2-like protein


Mass: 17569.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10
#12: Protein G10 protein


Mass: 35590.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KB76
#14: Protein Spliceosome-associated CWC15-like protein


Mass: 22580.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KWX5
#15: Protein Cell division control protein


Mass: 89110.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KDH5
#16: Protein CWF21 domain-containing protein


Mass: 21499.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640K740
#17: Protein Crooked neck-like protein 1


Mass: 93722.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KV53
#19: Protein RNA helicase


Mass: 123210.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KVV3, RNA helicase
#20: Protein U2 small nuclear ribonucleoprotein 40K, putative


Mass: 34821.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KNR9
#22: Protein NF-kappa-B-activating protein C-terminal domain-containing protein


Mass: 43596.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KXH6
#23: Protein MI domain-containing protein


Mass: 65686.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KX85
#26: Protein Uncharacterized protein


Mass: 27783.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KDU3
#27: Protein PRP19-related complex protein 3


Mass: 45326.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KRN7
#28: Protein Unspecified product


Mass: 18754.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KWM9
#29: Protein SNW domain-containing protein 1


Mass: 57655.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10
#30: Protein peptidylprolyl isomerase


Mass: 20554.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KHX2, peptidylprolyl isomerase
#33: Protein Zinc knuckle


Mass: 16757.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KSY0
#35: Protein
Pre-mRNA-processing factor 19


Mass: 53716.508 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10
References: UniProt: A0A640KLK2, RING-type E3 ubiquitin transferase
#36: Protein Probable RNA helicase


Mass: 128353.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10
#40: Protein U6 snRNA-associated Sm-like protein LSm4


Mass: 12885.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KQL9
#43: Protein Lsm7p protein, putative


Mass: 9968.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KI01
#48: Protein Lsm5p, putative


Mass: 13888.849 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KNU1
#51: Protein Sm protein F


Mass: 8533.749 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KUD7
#52: Protein Sm protein G


Mass: 8810.194 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KQ84
#54: Protein Sm protein B


Mass: 11872.810 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KQU2

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RRM domain-containing ... , 2 types, 2 molecules L8LY

#2: Protein RRM domain-containing protein


Mass: 17154.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KP41
#21: Protein RRM domain-containing protein


Mass: 13295.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KKX2

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Small nuclear ... , 6 types, 13 molecules LC2451U12552U22D2H5EUE53U3

#6: Protein Small nuclear ribonucleoprotein component-like protein


Mass: 110616.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KRB5
#46: Protein Small nuclear ribonucleoprotein, putative


Mass: 11214.814 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KHR4
#47: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 11798.734 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KR16
#49: Protein Small nuclear ribonucleaoprotein, putative


Mass: 16127.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KZZ6
#50: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E


Mass: 9926.351 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KLY5
#53: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 12345.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KTK0

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Guanine nucleotide-binding protein subunit beta-like ... , 3 types, 3 molecules LJLNSO

#11: Protein Guanine nucleotide-binding protein subunit beta-like protein


Mass: 55427.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KWH7
#13: Protein Guanine nucleotide-binding protein subunit beta-like protein


Mass: 33586.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KKK2
#31: Protein Guanine nucleotide-binding protein subunit beta-like protein


Mass: 68007.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KJ83

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Pre-mRNA-splicing factor ... , 5 types, 5 molecules LTSCSDSPSS

#18: Protein Pre-mRNA-splicing factor SYF1


Mass: 89299.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KGK2
#24: Protein Pre-mRNA-splicing factor SLU7


Mass: 46469.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KB40
#25: Protein Pre-mRNA-splicing factor 18


Mass: 59023.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KFR7
#32: Protein Pre-mRNA-splicing factor ISY1 homolog


Mass: 31012.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KE26
#34: Protein Pre-mRNA-splicing factor SPF27


Mass: 31636.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KPK5

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Protein/peptide , 1 types, 1 molecules UX

#37: Protein/peptide Unidentified protein


Mass: 1805.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10

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LSM domain-containing ... , 2 types, 2 molecules 6265

#38: Protein LSM domain-containing protein


Mass: 20523.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KDV9
#41: Protein LSM domain-containing protein


Mass: 15939.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KR67

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Sm domain-containing ... , 3 types, 3 molecules 636668

#39: Protein Sm domain-containing protein


Mass: 14153.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640K801
#42: Protein Sm domain-containing protein


Mass: 8616.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640K754
#44: Protein Sm domain-containing protein


Mass: 14105.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KIZ1

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RNA chain , 6 types, 6 molecules RNLELON2N5N6

#45: RNA chain Y-branched pre-mRNA


Mass: 13704.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10
#55: RNA chain SL RNA exon


Mass: 12361.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10
#56: RNA chain SL RNA outron


Mass: 18331.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: GenBank: 312489
#57: RNA chain U2 snRNA


Mass: 45393.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: GenBank: 15822519
#58: RNA chain U5 snRNA


Mass: 22591.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: GenBank: 2624234246
#59: RNA chain U6 snRNA


Mass: 32113.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: GenBank: 15824497

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Non-polymers , 8 types, 23 molecules

#60: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#61: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#62: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#63: 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
#64: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#65: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#66: Chemical ChemComp-GTG / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / MRNA CAP ANALOG N7-METHYL GPPPG


Mass: 803.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O18P3
#67: Chemical ChemComp-G5J / 5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine


Mass: 537.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O14P3

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Details

Has ligand of interestN
Has protein modificationY

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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: Leishmania tarentolae trans-spliceosome activated for catalytic step II (C* complex)
Type: COMPLEX / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 31410
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2SerialEMimage acquisition
4cryoSPARC4.6.0CTF correction
9PHENIX1.19.1model refinement
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
12cryoSPARC4.6.0classification
13RELION5classification
14cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1214398
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 325589 / Symmetry type: POINT

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