9IF7 image
Deposition Date 2025-02-17
Release Date 2026-09-02
Last Version Date 2026-10-07
Entry Detail
PDB ID:
9IF7
Keywords:
SPLICING
Title:
Cryo-EM structure of the kinetoplastid trans-spliceosome activated for catalytic step II (C* complex)
Biological Source:
Source Organism(s):
Leishmania tarentolae (Taxon ID: 5689)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9IF7 validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):LtaPh_2210200
Chain IDs:WA (auth: 24), DB (auth: 51), PB (auth: U1)
Chain Length:102
Number of Molecules:3
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KHR4
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):LtaPh_3334400
Chain IDs:XA (auth: 25), EB (auth: 52), QB (auth: U2)
Chain Length:103
Number of Molecules:3
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KR16
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Lsm5p, putative
Gene (Uniprot):LtaPh_3030100
Chain IDs:YA (auth: 2C)
Chain Length:128
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KNU1
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleaoprot
Gene (Uniprot):LtaPh_3605300
Chain IDs:ZA (auth: 2D)
Chain Length:141
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KZZ6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):LtaPh_3013200
Chain IDs:AB (auth: 2H), HB (auth: 5E), TB (auth: UE)
Chain Length:86
Number of Molecules:3
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KLY5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sm protein F
Gene (Uniprot):LtaPh_3544800
Chain IDs:BB (auth: 2I), IB (auth: 5F), UB (auth: UF)
Chain Length:76
Number of Molecules:3
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KUD7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sm protein G
Gene (Uniprot):LtaPh_3211600
Chain IDs:CB (auth: 2J), JB (auth: 5G), VB (auth: UG)
Chain Length:81
Number of Molecules:3
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KQ84
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):LtaPh_3438000
Chain IDs:FB (auth: 53), RB (auth: U3)
Chain Length:113
Number of Molecules:2
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KTK0
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sm protein B
Gene (Uniprot):LtaPh_2720600
Chain IDs:GB (auth: 5B), SB (auth: UB)
Chain Length:111
Number of Molecules:2
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KQU2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:LSM domain-containing protein
Gene (Uniprot):LtaPh_1612400
Chain IDs:OA (auth: 62)
Chain Length:190
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KDV9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sm domain-containing protein
Gene (Uniprot):LtaPh_0505300
Chain IDs:PA (auth: 63)
Chain Length:134
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640K801
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM4
Chain IDs:QA (auth: 64)
Chain Length:116
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KQL9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:LSM domain-containing protein
Gene (Uniprot):LtaPh_2810400
Chain IDs:RA (auth: 65)
Chain Length:151
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KR67
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sm domain-containing protein
Gene (Uniprot):LtaPh_0101600
Chain IDs:SA (auth: 66)
Chain Length:80
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640K754
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Lsm7p protein, putative
Gene (Uniprot):LtaPh_2600100
Chain IDs:TA (auth: 67)
Chain Length:91
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KI01
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sm domain-containing protein
Gene (Uniprot):LtaPh_2517900
Chain IDs:UA (auth: 68)
Chain Length:131
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KIZ1
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable eukaryotic initiatio
Gene (Uniprot):LtaPh_2815900
Chain IDs:A (auth: L7)
Chain Length:389
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KRB9 EC:3.6.4.13
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:RRM domain-containing protein
Gene (Uniprot):LtaPh_2607300
Chain IDs:B (auth: L8)
Chain Length:153
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KP41
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mago nashi-like protein,putat
Gene (Uniprot):LtaPh_3036000
Chain IDs:C (auth: L9)
Chain Length:162
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KMM3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Prp8 protein homologue, putat
Gene (Uniprot):LtaPh_3539600
Chain IDs:D (auth: LA)
Chain Length:2427
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KTJ2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase, p
Gene (Uniprot):LtaPh_1710900
Chain IDs:E (auth: LB)
Chain Length:2367
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KDJ4
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):LtaPh_3223800
Chain IDs:F (auth: LC)
Chain Length:1016
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KRB5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:PRKR-interacting protein 1
Gene (Uniprot):LtaPh_0406000
Chain IDs:G (auth: LD)
Chain Length:166
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KD47
Polymer Type:polyribonucleotide
Molecule:SL RNA exon
Chain IDs:KB (auth: LE)
Chain Length:39
Number of Molecules:1
Biological Source:Leishmania tarentolae
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor Cactin C-term
Gene (Uniprot):LtaPh_2824100
Chain IDs:H (auth: LF)
Chain Length:706
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KRR3
Polymer Type:polypeptide(L)
Molecule:RNA-binding motif protein
Chain IDs:I (auth: LG)
Chain Length:82
Number of Molecules:1
Biological Source:Leishmania tarentolae
Polymer Type:polypeptide(L)
Molecule:Splicing regulator SDE2-like
Chain IDs:J (auth: LH)
Chain Length:159
Number of Molecules:1
Biological Source:Leishmania tarentolae
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding pr
Gene (Uniprot):LtaPh_3649600
Chain IDs:K (auth: LJ)
Chain Length:509
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KWH7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:G10 protein
Gene (Uniprot):LtaPh_0902600
Chain IDs:L (auth: LL)
Chain Length:326
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KB76
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding pr
Gene (Uniprot):LtaPh_2829800
Chain IDs:M (auth: LN)
Chain Length:322
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KKK2
Polymer Type:polyribonucleotide
Molecule:SL RNA outron
Chain IDs:LB (auth: LO)
Chain Length:57
Number of Molecules:1
Biological Source:Leishmania tarentolae
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spliceosome-associated CWC15-
Gene (Uniprot):LtaPh_9904201
Chain IDs:N (auth: LP)
Chain Length:207
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KWX5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cell division control protein
Gene (Uniprot):LtaPh_1708300
Chain IDs:O (auth: LQ)
Chain Length:804
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KDH5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:CWF21 domain-containing prote
Gene (Uniprot):LtaPh_0101900
Chain IDs:P (auth: LR)
Chain Length:197
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640K740
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Crooked neck-like protein 1
Gene (Uniprot):LtaPh_3644200
Chain IDs:Q (auth: LS)
Chain Length:824
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KV53
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SYF1
Gene (Uniprot):LtaPh_2319600
Chain IDs:R (auth: LT)
Chain Length:794
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KGK2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA helicase
Gene (Uniprot):LtaPh_3629000
Chain IDs:S (auth: LV)
Chain Length:1087
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KVV3 EC:3.6.4.13
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 small nuclear ribonucleopr
Gene (Uniprot):LtaPh_3201800
Chain IDs:T (auth: LW)
Chain Length:307
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KNR9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:RRM domain-containing protein
Gene (Uniprot):LtaPh_2909200, LtaPh_2909931
Chain IDs:U (auth: LY)
Chain Length:114
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KKX2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:NF-kappa-B-activating protein
Gene (Uniprot):LtaPh_3306200, LtaPh_9910501
Chain IDs:V (auth: LZ)
Chain Length:403
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KXH6
Polymer Type:polyribonucleotide
Molecule:U2 snRNA
Chain IDs:MB (auth: N2)
Chain Length:142
Number of Molecules:1
Biological Source:Leishmania tarentolae
Polymer Type:polyribonucleotide
Molecule:U5 snRNA
Chain IDs:NB (auth: N5)
Chain Length:71
Number of Molecules:1
Biological Source:Leishmania tarentolae
Polymer Type:polyribonucleotide
Molecule:U6 snRNA
Chain IDs:OB (auth: N6)
Chain Length:100
Number of Molecules:1
Biological Source:Leishmania tarentolae
Polymer Type:polyribonucleotide
Molecule:Y-branched pre-mRNA
Chain IDs:VA (auth: RN)
Chain Length:68
Number of Molecules:1
Biological Source:Leishmania tarentolae
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:MI domain-containing protein
Gene (Uniprot):LtaPh_3652800
Chain IDs:W (auth: SA)
Chain Length:564
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KX85
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SLU7
Gene (Uniprot):LtaPh_0809200
Chain IDs:X (auth: SC)
Chain Length:417
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KB40
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor 18
Gene (Uniprot):LtaPh_2208700
Chain IDs:Y (auth: SD)
Chain Length:546
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KFR7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):LtaPh_1601800
Chain IDs:Z (auth: SF)
Chain Length:258
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KDU3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:PRP19-related complex protein
Gene (Uniprot):LtaPh_3331300
Chain IDs:AA (auth: SJ)
Chain Length:414
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KRN7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Unspecified product
Gene (Uniprot):LtaPh_3322300
Chain IDs:BA (auth: SK)
Chain Length:175
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KWM9
Polymer Type:polypeptide(L)
Molecule:SNW domain-containing protein
Chain IDs:CA (auth: SL)
Chain Length:544
Number of Molecules:1
Biological Source:Leishmania tarentolae
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:peptidylprolyl isomerase
Gene (Uniprot):LtaPh_2301500
Chain IDs:DA (auth: SN)
Chain Length:192
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KHX2 EC:5.2.1.8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding pr
Gene (Uniprot):LtaPh_2519400
Chain IDs:EA (auth: SO)
Chain Length:621
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KJ83
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor ISY1
Gene (Uniprot):LtaPh_0700200
Chain IDs:FA (auth: SP)
Chain Length:269
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KE26
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Zinc knuckle
Gene (Uniprot):LtaPh_3441400
Chain IDs:GA (auth: SQ)
Chain Length:150
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KSY0
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SPF2
Gene (Uniprot):LtaPh_3209700
Chain IDs:HA (auth: SS)
Chain Length:284
Number of Molecules:1
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KPK5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 19
Gene (Uniprot):LtaPh_2726100
Chain IDs:IA (auth: ST), JA (auth: SU), KA (auth: SV), LA (auth: SW)
Chain Length:513
Number of Molecules:4
Biological Source:Leishmania tarentolae
UniProt ID:A0A640KLK2 EC:2.3.2.27
Polymer Type:polypeptide(L)
Molecule:Probable RNA helicase
Chain IDs:MA (auth: TN)
Chain Length:1181
Number of Molecules:1
Biological Source:Leishmania tarentolae
Polymer Type:polypeptide(L)
Molecule:Unidentified protein
Chain IDs:NA (auth: UX)
Chain Length:21
Number of Molecules:1
Biological Source:Leishmania tarentolae
Ligand Molecules
ADP
G5J
GTG
GTP
IHP
K
MG
ZN
Primary Citation
Structural basis of step II spliced leader RNA trans-splicing in trypanosomatid parasites.
Nat Commun 17 ? ? (2026)
PMID: 42778629 DOI: 10.1038/s41467-026-77480-6

Abstact

Messenger RNA (mRNA) synthesis is fundamental to eukaryotic gene expression. In kinetoplastid parasites, including the human pathogens Trypanosoma and Leishmania, mRNAs are produced through a mechanism called Spliced Leader (SL) RNA trans-splicing. In this process, a short SL exon from a small noncoding RNA is joined to the 5' end of every mRNA, ensuring transcript stability and translation. Despite decades of study, the structural and mechanistic basis of SL trans-splicing remains elusive. Here, we report cryogenic electron microscopy structures of step II SL trans-splicing machineries from Leishmania tarentolae. These structures reveal the molecular mechanism of SL exon ligation and uncover lineage-specific adaptations that remodel the trypanosomatid trans-spliceosome for SL trans-splicing while preserving fundamental spliceosomal chemistry. Altogether, our results establish a mechanistic framework for SL trans-splicing and illuminate the evolutionary diversification of RNA processing in deeply diverged eukaryotes.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
9IF7
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