6URG

Cryo-EM structure of human CPSF160-WDR33-CPSF30-CPSF100 PIM complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Insights into the Human Pre-mRNA 3'-End Processing Machinery.

Zhang, Y.Sun, Y.Shi, Y.Walz, T.Tong, L.

(2020) Mol Cell 77: 800

  • DOI: https://doi.org/10.1016/j.molcel.2019.11.005
  • Primary Citation of Related Structures:  
    6URG, 6URO

  • PubMed Abstract: 

    The mammalian pre-mRNA 3'-end-processing machinery consists of cleavage and polyadenylation specificity factor (CPSF), cleavage stimulation factor (CstF), and other proteins, but the overall architecture of this machinery remains unclear. CPSF contains two functionally distinct modules: a cleavage factor (mCF) and a polyadenylation specificity factor (mPSF). Here, we have produced recombinant human CPSF and CstF and examined these factors by electron microscopy (EM). We find that mPSF is the organizational core of the machinery, while the conformations of mCF and CstF and the position of mCF relative to mPSF are highly variable. We have identified by cryo-EM a segment in CPSF100 that tethers mCF to mPSF, and we have named it the PSF interaction motif (PIM). Mutations in the PIM can abolish CPSF formation, indicating that it is a crucial contact in CPSF. We have also obtained reconstructions of mCF and CstF77 by cryo-EM, assembled around the mPSF core.


  • Organizational Affiliation

    Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY 10065, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 11,443Homo sapiensMutation(s): 0 
Gene Names: CPSF1CPSF160
UniProt & NIH Common Fund Data Resources
Find proteins for Q10570 (Homo sapiens)
Explore Q10570 
Go to UniProtKB:  Q10570
PHAROS:  Q10570
GTEx:  ENSG00000071894 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10570
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
pre-mRNA 3' end processing protein WDR33587Homo sapiensMutation(s): 0 
Gene Names: WDR33WDC146
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0J8 (Homo sapiens)
Explore Q9C0J8 
Go to UniProtKB:  Q9C0J8
PHAROS:  Q9C0J8
GTEx:  ENSG00000136709 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C0J8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 4250Homo sapiensMutation(s): 0 
Gene Names: CPSF4CPSF30NARNEB1
UniProt & NIH Common Fund Data Resources
Find proteins for O95639 (Homo sapiens)
Explore O95639 
Go to UniProtKB:  O95639
PHAROS:  O95639
GTEx:  ENSG00000160917 
Entity Groups  
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UniProt GroupO95639
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 2D [auth F]782Homo sapiensMutation(s): 0 
Gene Names: CPSF2CPSF100KIAA1367
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2I0 (Homo sapiens)
Explore Q9P2I0 
Go to UniProtKB:  Q9P2I0
PHAROS:  Q9P2I0
GTEx:  ENSG00000165934 
Entity Groups  
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UniProt GroupQ9P2I0
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



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: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2020-03-04
    Changes: Database references
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references