6R5K

Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 of the entry. See complete history


Literature

Molecular Basis for poly(A) RNP Architecture and Recognition by the Pan2-Pan3 Deadenylase.

Schafer, I.B.Yamashita, M.Schuller, J.M.Schussler, S.Reichelt, P.Strauss, M.Conti, E.

(2019) Cell 177: 1619

  • DOI: https://doi.org/10.1016/j.cell.2019.04.013
  • Primary Citation of Related Structures:  
    6R5K

  • PubMed Abstract: 

    The stability of eukaryotic mRNAs is dependent on a ribonucleoprotein (RNP) complex of poly(A)-binding proteins (PABPC1/Pab1) organized on the poly(A) tail. This poly(A) RNP not only protects mRNAs from premature degradation but also stimulates the Pan2-Pan3 deadenylase complex to catalyze the first step of poly(A) tail shortening. We reconstituted this process in vitro using recombinant proteins and show that Pan2-Pan3 associates with and degrades poly(A) RNPs containing two or more Pab1 molecules. The cryo-EM structure of Pan2-Pan3 in complex with a poly(A) RNP composed of 90 adenosines and three Pab1 protomers shows how the oligomerization interfaces of Pab1 are recognized by conserved features of the deadenylase and thread the poly(A) RNA substrate into the nuclease active site. The structure reveals the basis for the periodic repeating architecture at the 3' end of cytoplasmic mRNAs. This illustrates mechanistically how RNA-bound Pab1 oligomers act as rulers for poly(A) tail length over the mRNAs' lifetime.


  • Organizational Affiliation

    Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany. Electronic address: ischaefe@biochem.mpg.de.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PAN2-PAN3 deadenylation complex catalytic subunit PAN21,115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PAN2YGL094C
EC: 3.1.13.4
UniProt
Find proteins for P53010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P53010
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UniProt GroupP53010
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyadenylate-binding protein, cytoplasmic and nuclearB [auth D],
D [auth F],
E [auth H]
581Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PAB1YER165W
UniProt
Find proteins for P04147 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P04147
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UniProt GroupP04147
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PAN2-PAN3 deadenylation complex subunit PAN3F [auth N]458Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PAN3ECM35YKL025C
UniProt
Find proteins for P36102 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36102 
Go to UniProtKB:  P36102
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UniProt GroupP36102
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PAN2-PAN3 deadenylation complex subunit PAN3G [auth O]689Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PAN3ECM35YKL025C
UniProt
Find proteins for P36102 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36102 
Go to UniProtKB:  P36102
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36102
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
poly(A) RNAC [auth E]90Saccharomyces cerevisiae S288C
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0-beta-1
MODEL REFINEMENTCoot0.8

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-18
    Changes: Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references, Derived calculations