9IF7 | pdb_00009if7

Cryo-EM structure of the kinetoplastid trans-spliceosome activated for catalytic step II (C* complex)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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: 2,816.28 kDa 
  • Atom Count: 135,855 
  • Modeled Residue Count: 17,809 
  • Deposited Residue Count: 24,640 
  • Unique protein chains: 53
  • Unique nucleic acid chains: 6

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable eukaryotic initiation factor 4AA [auth L7]389Leishmania tarentolaeMutation(s): 0 
EC: 3.6.4.13
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RRM domain-containing proteinB [auth L8]153Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Mago nashi-like protein,putativeC [auth L9]162Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Prp8 protein homologue, putativeD [auth LA]2,427Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase, putativeE [auth LB]2,367Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein component-like proteinF [auth LC]1,016Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
PRKR-interacting protein 1G [auth LD]166Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing factor Cactin C-terminal domain-containing proteinH [auth LF]706Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-binding motif proteinI [auth LG]82Leishmania tarentolaeMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Splicing regulator SDE2-like proteinJ [auth LH]159Leishmania tarentolaeMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinK [auth LJ]509Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
G10 proteinL [auth LL]326Leishmania tarentolaeMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinM [auth LN]322Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Spliceosome-associated CWC15-like proteinN [auth LP]207Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division control proteinO [auth LQ]804Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
CWF21 domain-containing proteinP [auth LR]197Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1Q [auth LS]824Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1R [auth LT]794Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA helicaseS [auth LV]1,087Leishmania tarentolaeMutation(s): 0 
EC: 3.6.4.13
UniProt
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein 40K, putativeT [auth LW]307Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
RRM domain-containing proteinU [auth LY]114Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
NF-kappa-B-activating protein C-terminal domain-containing proteinV [auth LZ]403Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
MI domain-containing proteinW [auth SA]564Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7X [auth SC]417Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 18Y [auth SD]546Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized proteinZ [auth SF]258Leishmania tarentolaeMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
PRP19-related complex protein 3AA [auth SJ]414Leishmania tarentolaeMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Unspecified productBA [auth SK]175Leishmania tarentolaeMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1CA [auth SL]544Leishmania tarentolaeMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
peptidylprolyl isomeraseDA [auth SN]192Leishmania tarentolaeMutation(s): 0 
EC: 5.2.1.8
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinEA [auth SO]621Leishmania tarentolaeMutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homologFA [auth SP]269Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc knuckleGA [auth SQ]150Leishmania tarentolaeMutation(s): 1 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27HA [auth SS]284Leishmania tarentolaeMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19IA [auth ST],
JA [auth SU],
KA [auth SV],
LA [auth SW]		513Leishmania tarentolaeMutation(s): 0 
EC: 2.3.2.27
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable RNA helicaseMA [auth TN]1,181Leishmania tarentolaeMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
Unidentified proteinNA [auth UX]21Leishmania tarentolaeMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
LSM domain-containing proteinOA [auth 62]190Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm domain-containing proteinPA [auth 63]134Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4QA [auth 64]116Leishmania tarentolaeMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
LSM domain-containing proteinRA [auth 65]151Leishmania tarentolaeMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm domain-containing proteinSA [auth 66]80Leishmania tarentolaeMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Lsm7p protein, putativeTA [auth 67]91Leishmania tarentolaeMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm domain-containing proteinUA [auth 68]131Leishmania tarentolaeMutation(s): 1 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein, putativeDB [auth 51],
PB [auth U1],
WA [auth 24]		102Leishmania tarentolaeMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2EB [auth 52],
QB [auth U2],
XA [auth 25]		103Leishmania tarentolaeMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
Lsm5p, putativeYA [auth 2C]128Leishmania tarentolaeMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleaoprotein, putativeZA [auth 2D]141Leishmania tarentolaeMutation(s): 0 
UniProt
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UniProt GroupA0A640KZZ6
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Reference Sequence
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EAB [auth 2H],
HB [auth 5E],
TB [auth UE]		86Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KLY5 (Leishmania tarentolae)
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UniProt GroupA0A640KLY5
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm protein FBB [auth 2I],
IB [auth 5F],
UB [auth UF]		76Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KUD7 (Leishmania tarentolae)
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UniProt GroupA0A640KUD7
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm protein GCB [auth 2J],
JB [auth 5G],
VB [auth UG]		81Leishmania tarentolaeMutation(s): 0 
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Find proteins for A0A640KQ84 (Leishmania tarentolae)
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UniProt GroupA0A640KQ84
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3FB [auth 53],
RB [auth U3]		113Leishmania tarentolaeMutation(s): 0 
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Find proteins for A0A640KTK0 (Leishmania tarentolae)
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
Sm protein BGB [auth 5B],
SB [auth UB]		111Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KQU2 (Leishmania tarentolae)
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Entity ID: 45
MoleculeChains LengthOrganismImage
Y-branched pre-mRNAVA [auth RN]68Leishmania tarentolae
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Entity ID: 55
MoleculeChains LengthOrganismImage
SL RNA exonKB [auth LE]39Leishmania tarentolae
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Entity ID: 56
MoleculeChains LengthOrganismImage
SL RNA outronLB [auth LO]57Leishmania tarentolae
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Entity ID: 57
MoleculeChains LengthOrganismImage
U2 snRNAMB [auth N2]142Leishmania tarentolae
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Entity ID: 58
MoleculeChains LengthOrganismImage
U5 snRNANB [auth N5]71Leishmania tarentolae
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Entity ID: 59
MoleculeChains LengthOrganismImage
U6 snRNAOB [auth N6]100Leishmania tarentolae
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTG

Query on GTG


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

Query on G5J


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

Query on ADP


Download:Ideal Coordinates CCD File
XB [auth L7]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
DC [auth LL],
EC [auth LL],
FC [auth LL],
GC [auth SC],
HC [auth SQ]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K

Query on K


Download:Ideal Coordinates CCD File
YB [auth L7]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
AC [auth LA]
CC [auth LC]
JC [auth N5]
LC [auth N6]
MC [auth N6]
AC [auth LA],
CC [auth LC],
JC [auth N5],
LC [auth N6],
MC [auth N6],
NC [auth N6],
OC [auth N6],
PC [auth N6],
QC [auth N6],
RC [auth N6],
SC [auth N6],
WB [auth L7]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP		CA [auth SL]L-PEPTIDE LINKINGC3 H8 N O6 PSER
UNK
Query on UNK		NA [auth UX]L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.1
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