9S2F | pdb_00009s2f

Human debranched intron spliceosome (DIS)

  • Classification: SPLICING
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-07-21 Released: 2026-07-29 
  • Deposition Author(s): Boreikaite, V., Vorlaender, M.K., Plaschka, C.
  • Funding Organization(s): European Molecular Biology Organization (EMBO), Human Frontier Science Program (HFSP), Austrian Science Fund, European Research Council (ERC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9S2F

This is version 1.0 of the entry. See complete history

Literature

Mechanisms of spliceosome termination

Boreikaite, V.Vorlaender, M.K.Phillips, A.W.Faraway, R.Opitz, L.Wanke, M.Raffl, G.Fin, L.Ameres, S.L.Plaschka, C.

To be published.

Macromolecule Content 

  • Total Structure Weight: 2,174.49 kDa 
  • Atom Count: 77,158 
  • Modeled Residue Count: 10,963 
  • Deposited Residue Count: 18,652 
  • Unique protein chains: 31
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DHX35A [auth 35]703Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H5Z1 (Homo sapiens)
Explore Q9H5Z1 
Go to UniProtKB:  Q9H5Z1
GTEx:  ENSG00000101452 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H5Z1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8C [auth A]2,335Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P2Q9 (Homo sapiens)
Explore Q6P2Q9 
Go to UniProtKB:  Q6P2Q9
GTEx:  ENSG00000174231 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P2Q9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseD [auth B]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O75643 (Homo sapiens)
Explore O75643 
Go to UniProtKB:  O75643
GTEx:  ENSG00000144028 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75643
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentE [auth C]972Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15029 (Homo sapiens)
Explore Q15029 
Go to UniProtKB:  Q15029
GTEx:  ENSG00000108883 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15029
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinF [auth E]357Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DI7 (Homo sapiens)
Explore Q96DI7 
Go to UniProtKB:  Q96DI7
GTEx:  ENSG00000060688 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96DI7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
G patch domain-containing protein 1G [auth GP]931Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRR8 (Homo sapiens)
Explore Q9BRR8 
Go to UniProtKB:  Q9BRR8
GTEx:  ENSG00000076650 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BRR8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1H [auth I]855Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCS7 (Homo sapiens)
Explore Q9HCS7 
Go to UniProtKB:  Q9HCS7
GTEx:  ENSG00000076924 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HCS7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1I [auth J]848Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZJ0 (Homo sapiens)
Explore Q9BZJ0 
Go to UniProtKB:  Q9BZJ0
GTEx:  ENSG00000101343 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZJ0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27J [auth K]225Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75934 (Homo sapiens)
Explore O75934 
Go to UniProtKB:  O75934
GTEx:  ENSG00000116752 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75934
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinK [auth L]802Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99459 (Homo sapiens)
Explore Q99459 
Go to UniProtKB:  Q99459
GTEx:  ENSG00000096401 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99459
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2L [auth M]243Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O95926 (Homo sapiens)
Explore O95926 
Go to UniProtKB:  O95926
GTEx:  ENSG00000117614 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95926
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein BUD31 homologM [auth N]144Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P41223 (Homo sapiens)
Explore P41223 
Go to UniProtKB:  P41223
GTEx:  ENSG00000106245 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41223
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22N [auth O]420Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NW64 (Homo sapiens)
Explore Q9NW64 
Go to UniProtKB:  Q9NW64
GTEx:  ENSG00000086589 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NW64
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologO [auth P]229Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P013 (Homo sapiens)
Explore Q9P013 
Go to UniProtKB:  Q9P013
GTEx:  ENSG00000150316 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P013
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Intron-binding protein aquariusP [auth Q]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O60306 (Homo sapiens)
Explore O60306 
Go to UniProtKB:  O60306
GTEx:  ENSG00000021776 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60306
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1Q [auth R]536Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13573 (Homo sapiens)
Explore Q13573 
Go to UniProtKB:  Q13573
GTEx:  ENSG00000100603 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13573
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1R [auth S]166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3C6 (Homo sapiens)
Explore Q9Y3C6 
Go to UniProtKB:  Q9Y3C6
GTEx:  ENSG00000137168 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3C6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1S [auth T]514Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O43660 (Homo sapiens)
Explore O43660 
Go to UniProtKB:  O43660
GTEx:  ENSG00000171566 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43660
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17T [auth W]579Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60508 (Homo sapiens)
Explore O60508 
Go to UniProtKB:  O60508
GTEx:  ENSG00000168438 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60508
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat domain-containing protein 83U [auth WD]315Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRX9 (Homo sapiens)
Explore Q9BRX9 
Go to UniProtKB:  Q9BRX9
GTEx:  ENSG00000123154 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BRX9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 12V [auth Z]166Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUD4 (Homo sapiens)
Explore Q8WUD4 
Go to UniProtKB:  Q8WUD4
GTEx:  ENSG00000160799 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUD4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3W [auth a]126Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62318 (Homo sapiens)
Explore P62318 
Go to UniProtKB:  P62318
GTEx:  ENSG00000100028 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62318
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'X [auth b]240Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P14678 (Homo sapiens)
Explore P14678 
Go to UniProtKB:  P14678
GTEx:  ENSG00000125835 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14678
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1Y [auth c]119Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62314 (Homo sapiens)
Explore P62314 
Go to UniProtKB:  P62314
GTEx:  ENSG00000167088 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62314
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2Z [auth d]118Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62316 (Homo sapiens)
Explore P62316 
Go to UniProtKB:  P62316
GTEx:  ENSG00000125743 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62316
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EAA [auth e]92Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62304 (Homo sapiens)
Explore P62304 
Go to UniProtKB:  P62304
GTEx:  ENSG00000182004 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62304
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FBA [auth f]86Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62306 (Homo sapiens)
Explore P62306 
Go to UniProtKB:  P62306
GTEx:  ENSG00000139343 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62306
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GCA [auth g]76Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62308 (Homo sapiens)
Explore P62308 
Go to UniProtKB:  P62308
GTEx:  ENSG00000143977 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62308
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19DA [auth q],
EA [auth r],
FA [auth s],
GA [auth t]
504Homo sapiensMutation(s): 0 
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMS4 (Homo sapiens)
Explore Q9UMS4 
Go to UniProtKB:  Q9UMS4
GTEx:  ENSG00000110107 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UMS4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EHA [auth y]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNP9 (Homo sapiens)
Explore Q9UNP9 
Go to UniProtKB:  Q9UNP9
GTEx:  ENSG00000084072 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNP9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homologIA [auth D]285Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULR0 (Homo sapiens)
Explore Q9ULR0 
Go to UniProtKB:  Q9ULR0
GTEx:  ENSG00000240682 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULR0
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNAB [auth 5]116Homo sapiens
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 33
MoleculeChains LengthOrganismImage
IntronJA [auth IN]10Homo sapiens
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 34
MoleculeChains LengthOrganismImage
U6 snRNAKA [auth 6]106Homo sapiens
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP

Query on IHP



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

Query on GTP



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

Query on ZN



Download:Ideal Coordinates CCD File
OA [auth N],
PA [auth N],
QA [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
NA [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
Q [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419+SVN
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)European UnionALTF 784-2023
Human Frontier Science Program (HFSP)FranceLT0013/2024-L
Austrian Science FundAustriaESP7844224
European Research Council (ERC)European UnionERC-2020-STG 949081
Austrian Science FundAustriaDOC177-B

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-29
    Type: Initial release