7AAV

Human pre-Bact-2 spliceosome core structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.

Townsend, C.Leelaram, M.N.Agafonov, D.E.Dybkov, O.Will, C.L.Bertram, K.Urlaub, H.Kastner, B.Stark, H.Luhrmann, R.

(2020) Science 370

  • DOI: 10.1126/science.abc3753
  • Primary Citation of Related Structures:  
    7AAV, 7ABF, 7ABG, 7ABH, 7ABI

  • PubMed Abstract: 
  • Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding ...

    Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-B act complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature B act complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA.


    Organizational Affiliation

    Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. reinhard.luehrmann@mpibpc.mpg.de hstark1@gwdg.de b.kastner@mpibpc.mpg.de.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentA [auth r]972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
UniProt & NIH Common Fund Data Resources
Find proteins for Q15029 (Homo sapiens)
Explore Q15029 
Go to UniProtKB:  Q15029
PHAROS:  Q15029
GTEx:  ENSG00000108883 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15029
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologB [auth Q]144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
UniProt & NIH Common Fund Data Resources
Find proteins for P41223 (Homo sapiens)
Explore P41223 
Go to UniProtKB:  P41223
PHAROS:  P41223
GTEx:  ENSG00000106245 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41223
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinC [auth L]802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
UniProt & NIH Common Fund Data Resources
Find proteins for Q99459 (Homo sapiens)
Explore Q99459 
Go to UniProtKB:  Q99459
PHAROS:  Q99459
GTEx:  ENSG00000096401 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99459
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologD [auth R]229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P013 (Homo sapiens)
Explore Q9P013 
Go to UniProtKB:  Q9P013
PHAROS:  Q9P013
GTEx:  ENSG00000150316 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P013
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Microfibrillar-associated protein 1E [auth K]439Homo sapiensMutation(s): 0 
Gene Names: MFAP1
UniProt & NIH Common Fund Data Resources
Find proteins for P55081 (Homo sapiens)
Explore P55081 
Go to UniProtKB:  P55081
PHAROS:  P55081
GTEx:  ENSG00000140259 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55081
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1F [auth G]514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
UniProt & NIH Common Fund Data Resources
Find proteins for O43660 (Homo sapiens)
Explore O43660 
Go to UniProtKB:  O43660
PHAROS:  O43660
GTEx:  ENSG00000171566 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43660
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17H [auth 8]579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
UniProt & NIH Common Fund Data Resources
Find proteins for O60508 (Homo sapiens)
Explore O60508 
Go to UniProtKB:  O60508
PHAROS:  O60508
GTEx:  ENSG00000168438 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60508
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38AI312Homo sapiensMutation(s): 0 
Gene Names: PRPF38A
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAV1 (Homo sapiens)
Explore Q8NAV1 
Go to UniProtKB:  Q8NAV1
PHAROS:  Q8NAV1
GTEx:  ENSG00000134748 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NAV1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8J [auth A]2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P2Q9 (Homo sapiens)
Explore Q6P2Q9 
Go to UniProtKB:  Q6P2Q9
PHAROS:  Q6P2Q9
GTEx:  ENSG00000174231 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P2Q9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22K [auth P]420Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NW64 (Homo sapiens)
Explore Q9NW64 
Go to UniProtKB:  Q9NW64
PHAROS:  Q9NW64
GTEx:  ENSG00000086589 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NW64
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1L [auth v]536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q13573 (Homo sapiens)
Explore Q13573 
Go to UniProtKB:  Q13573
PHAROS:  Q13573
GTEx:  ENSG00000100603 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13573
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger matrin-type protein 2M [auth N]199Homo sapiensMutation(s): 0 
Gene Names: ZMAT2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96NC0 (Homo sapiens)
Explore Q96NC0 
Go to UniProtKB:  Q96NC0
PHAROS:  Q96NC0
GTEx:  ENSG00000146007 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96NC0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein 5Q [auth q]73Homo sapiensMutation(s): 0 
Gene Names: UBL5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZL1 (Homo sapiens)
Explore Q9BZL1 
Go to UniProtKB:  Q9BZL1
PHAROS:  Q9BZL1
GTEx:  ENSG00000198258 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZL1
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
MINX M3 pre-mRNAG [auth Z]230synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChainsLengthOrganismImage
U2 snRNAN [auth 2]188Homo sapiens
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChainsLengthOrganismImage
U5 snRNAO [auth 5]116Homo sapiens
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChainsLengthOrganismImage
U6 snRNAP [auth 6]106Homo sapiens
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KGN
Query on KGN

Download Ideal Coordinates CCD File 
T [auth A]D-chiro inositol hexakisphosphate
C6 H18 O24 P6
IMQLKJBTEOYOSI-LKPKBOIGSA-N
 Ligand Interaction
GTP
Query on GTP

Download Ideal Coordinates CCD File 
R [auth r]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
S [auth r]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany860

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references