9IF8 | pdb_00009if8

Cryo-EM structure of the kinetoplastid post-catalytic trans-spliceosome (P complex)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.0 of the entry. See complete history. 

Literature

Structural basis for kinetoplastid SL trans-splicing

Nadenoen, T., Vanden Broeck, A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 2,719.09 kDa 
  • Atom Count: 128,394 
  • Modeled Residue Count: 16,901 
  • Deposited Residue Count: 23,786 
  • Unique protein chains: 48
  • Unique nucleic acid chains: 7

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prp8 protein homologue, putativeA [auth LA]2,427Leishmania tarentolaeMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase, putativeB [auth LB]2,367Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein component-like proteinC [auth LC]1,016Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PRKR-interacting protein 1D [auth LD]166Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor Cactin C-terminal domain-containing proteinE [auth LF]706Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-binding motif proteinF [auth LG]82Leishmania tarentolaeMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing regulator SDE2-like proteinG [auth LH]159Leishmania tarentolaeMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinH [auth LJ]509Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
G10 proteinI [auth LL]326Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinJ [auth LN]322Leishmania tarentolaeMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Spliceosome-associated CWC15-like proteinK [auth LP]207Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division control proteinL [auth LQ]804Leishmania tarentolaeMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
CWF21 domain-containing proteinM [auth LR]197Leishmania tarentolaeMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1N [auth LS]824Leishmania tarentolaeMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1O [auth LT]794Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA helicaseP [auth LV]1,087Leishmania tarentolaeMutation(s): 0 
EC: 3.6.4.13
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein 40K, putativeQ [auth LW]307Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
RRM domain-containing proteinR [auth LY]114Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
NF-kappa-B-activating protein C-terminal domain-containing proteinS [auth LZ]403Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
MI domain-containing proteinT [auth SA]564Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7U [auth SC]417Leishmania tarentolaeMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 18V [auth SD]546Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized proteinW [auth SF]258Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
PRP19-related complex protein 3X [auth SJ]414Leishmania tarentolaeMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Unspecified productY [auth SK]175Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1Z [auth SL]544Leishmania tarentolaeMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
peptidylprolyl isomeraseAA [auth SN]192Leishmania tarentolaeMutation(s): 0 
EC: 5.2.1.8
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinBA [auth SO]621Leishmania tarentolaeMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homologCA [auth SP]269Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27DA [auth SS]284Leishmania tarentolaeMutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19EA [auth ST],
FA [auth SU],
GA [auth SV],
HA [auth SW]		513Leishmania tarentolaeMutation(s): 0 
EC: 2.3.2.27
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable RNA helicaseIA [auth TN]1,181Leishmania tarentolaeMutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
LSM domain-containing proteinKA [auth 62]190Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm domain-containing proteinLA [auth 63]134Leishmania tarentolaeMutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4MA [auth 64]116Leishmania tarentolaeMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
LSM domain-containing proteinNA [auth 65]151Leishmania tarentolaeMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm domain-containing proteinOA [auth 66]80Leishmania tarentolaeMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Lsm7p protein, putativePA [auth 67]91Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm domain-containing proteinQA [auth A]131Leishmania tarentolaeMutation(s): 1 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein, putativeLB [auth U1],
SA [auth 24],
ZA [auth 51]		102Leishmania tarentolaeMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2AB [auth 52],
MB [auth U2],
TA [auth 25]		103Leishmania tarentolaeMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
Lsm5p, putativeUA [auth 2C]128Leishmania tarentolaeMutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleaoprotein, putativeVA [auth 2D]141Leishmania tarentolaeMutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EDB [auth 5E],
PB [auth UE],
WA [auth 2H]		86Leishmania tarentolaeMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm protein FEB [auth 5F],
QB [auth UF],
XA [auth 2I]		76Leishmania tarentolaeMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm protein GFB [auth 5G],
RB [auth UG],
YA [auth 2J]		81Leishmania tarentolaeMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3BB [auth 53],
NB [auth U3]		113Leishmania tarentolaeMutation(s): 0 
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UniProt GroupA0A640KTK0
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Reference Sequence
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|  3D Structure
Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm protein BCB [auth 5B],
OB [auth UB]		111Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KQU2 (Leishmania tarentolae)
Explore A0A640KQU2 
Go to UniProtKB:  A0A640KQU2
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UniProt GroupA0A640KQU2
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Reference Sequence
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Entity ID: 33
MoleculeChains LengthOrganismImage
Unidentified proteinJA [auth UX]21Leishmania tarentolae
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Reference Sequence
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Entity ID: 41
MoleculeChains LengthOrganismImage
Y-branched pre-mRNARA [auth RN]44Leishmania tarentolae
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Entity ID: 51
MoleculeChains LengthOrganismImage
SL-ligated pre-mRNAGB [auth LE]63Leishmania tarentolae
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Entity ID: 52
MoleculeChains LengthOrganismImage
SL RNA outronHB [auth LO]57Leishmania tarentolae
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Entity ID: 53
MoleculeChains LengthOrganismImage
U2 snRNAIB [auth N2]142Leishmania tarentolae
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Entity ID: 54
MoleculeChains LengthOrganismImage
U5 snRNAJB [auth N5]71Leishmania tarentolae
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Entity ID: 55
MoleculeChains LengthOrganismImage
U6 snRNAKB [auth N6]100Leishmania tarentolae
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTG

Query on GTG


Download:Ideal Coordinates CCD File
CC [auth N5]7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
C21 H30 N10 O18 P3
FHHZHGZBHYYWTG-INFSMZHSSA-O
IHP

Query on IHP


Download:Ideal Coordinates CCD File
SB [auth LA]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
G5J

Query on G5J


Download:Ideal Coordinates CCD File
EC [auth N6]5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine
C11 H18 N5 O14 P3
DJZJYVFASQUZKQ-KQYNXXCUSA-N
GTP

Query on GTP


Download:Ideal Coordinates CCD File
UB [auth LC]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
WB [auth LL],
XB [auth LL],
YB [auth LL],
ZB [auth SC]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
AC [auth LE]
BC [auth N2]
DC [auth N5]
FC [auth N6]
GC [auth N6]
AC [auth LE],
BC [auth N2],
DC [auth N5],
FC [auth N6],
GC [auth N6],
HC [auth N6],
IC [auth N6],
JC [auth N6],
KC [auth N6],
LC [auth N6],
TB [auth LA],
VB [auth LC]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP		Z [auth SL]L-PEPTIDE LINKINGC3 H8 N O6 PSER
UNK
Query on UNK		JA [auth UX]L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.6.0

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Fonds National de la Recherche Scientifique (FNRS)BelgiumMISU F.6005.25
European Research Council (ERC)European UnionTranSplice 101162011

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-02
    Type: Initial release