6DNH

Cryo-EM structure of human CPSF-160-WDR33-CPSF-30-PAS RNA complex at 3.4 A resolution

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Molecular basis for the recognition of the human AAUAAA polyadenylation signal.

Sun, Y., Zhang, Y., Hamilton, K., Manley, J.L., Shi, Y., Walz, T., Tong, L.

(2018) Proc Natl Acad Sci U S A 115: E1419-E1428

  • DOI: https://doi.org/10.1073/pnas.1718723115
  • Primary Citation of Related Structures:  
    6BLY, 6BM0, 6DNH

  • PubMed Abstract: 

    • Nearly all eukaryotic messenger RNA precursors must undergo cleavage and polyadenylation at their 3'-end for maturation. A crucial step in this process is the recognition of the AAUAAA polyadenylation signal (PAS), and the molecular mechanism of this recognition has been a long-standing problem ...

    Nearly all eukaryotic messenger RNA precursors must undergo cleavage and polyadenylation at their 3'-end for maturation. A crucial step in this process is the recognition of the AAUAAA polyadenylation signal (PAS), and the molecular mechanism of this recognition has been a long-standing problem. Here, we report the cryo-electron microscopy structure of a quaternary complex of human CPSF-160, WDR33, CPSF-30, and an AAUAAA RNA at 3.4-Å resolution. Strikingly, the AAUAAA PAS assumes an unusual conformation that allows this short motif to be bound directly by both CPSF-30 and WDR33. The A1 and A2 bases are recognized specifically by zinc finger 2 (ZF2) of CPSF-30 and the A4 and A5 bases by ZF3. Interestingly, the U3 and A6 bases form an intramolecular Hoogsteen base pair and directly contact WDR33. CPSF-160 functions as an essential scaffold and preorganizes CPSF-30 and WDR33 for high-affinity binding to AAUAAA. Our findings provide an elegant molecular explanation for how PAS sequences are recognized for mRNA 3'-end formation.

    Organizational Affiliation: 

    Department of Biological Sciences, Columbia University, New York, NY 10027; jlm2@columbia.edu twalz@mail.rockefeller.edu ltong@columbia.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 11,443Homo sapiensMutation(s): 0 
Gene Names: CPSF1, CPSF160
UniProt & NIH Common Fund Data Resources
Find proteins for Q10570 (Homo sapiens)
Explore Q10570 
Go to UniProtKB:  Q10570
PHAROS:  Q10570
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UniProt GroupQ10570
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
pre-mRNA 3' end processing protein WDR33587Homo sapiensMutation(s): 0 
Gene Names: WDR33, WDC146
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0J8 (Homo sapiens)
Explore Q9C0J8 
Go to UniProtKB:  Q9C0J8
PHAROS:  Q9C0J8
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UniProt GroupQ9C0J8
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 4245Homo sapiensMutation(s): 0 
Gene Names: CPSF4, CPSF30, NAR, NEB1
UniProt & NIH Common Fund Data Resources
Find proteins for O95639 (Homo sapiens)
Explore O95639 
Go to UniProtKB:  O95639
PHAROS:  O95639
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UniProt GroupO95639
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*AP*UP*AP*AP*AP*C)-3')D [auth E]17Betapolyomavirus macacae
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth C],
F [auth C],
G [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118093

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence