6XKB

Crystal structure of SR-related and CTD-associated factor 4(SCAF4-CID)with peptide S2,S5p-CTD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis for the recognition of the S2, S5-phosphorylated RNA polymerase II CTD by the mRNA anti-terminator protein hSCAF4.

Zhou, M.Ehsan, F.Gan, L.Dong, A.Li, Y.Liu, K.Min, J.

(2022) FEBS Lett 596: 249-259

  • DOI: 10.1002/1873-3468.14256
  • Primary Citation of Related Structures:  
    6XKB

  • PubMed Abstract: 
  • The C-terminal domain (CTD) of RNA polymerase II serves as a binding platform for numerous enzymes and transcription factors involved in nascent RNA processing and the transcription cycle. The S2, S5-phosphorylated CTD is recognized by the transcription factor SCAF4, which functions as a transcription anti-terminator by preventing early mRNA transcript cleavage and polyadenylation ...

    The C-terminal domain (CTD) of RNA polymerase II serves as a binding platform for numerous enzymes and transcription factors involved in nascent RNA processing and the transcription cycle. The S2, S5-phosphorylated CTD is recognized by the transcription factor SCAF4, which functions as a transcription anti-terminator by preventing early mRNA transcript cleavage and polyadenylation. Here, we measured the binding affinities of differently modified CTD peptides by hSCAF4 and solved the complex structure of the hSCAF4-CTD-interaction domain (CID) bound to a S2, S5-quadra-phosphorylated CTD peptide. Our results revealed that the S2, S5-quadra-phosphorylated CTD peptide adopts a trans conformation and is located in a positively charged binding groove of hSCAF4-CID. Although hSCAF4-CID has almost the same binding pattern to the CTD as other CID-containing proteins, it preferentially binds to the S2, S5-phosphorylated CTD. Our findings provide insight into the regulatory mechanism of hSCAF4 in transcription termination.


    Organizational Affiliation

    Department of Physiology, University of Toronto, Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SR-related and CTD-associated factor 4A, B, C, D, E140Homo sapiensMutation(s): 0 
Gene Names: SCAF4KIAA1172SFRS15
UniProt & NIH Common Fund Data Resources
Find proteins for O95104 (Homo sapiens)
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PHAROS:  O95104
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UniProt GroupO95104
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S2,S5p-CTD peptideF,
G,
H [auth I],
I [auth J],
J [auth K]
20Homo sapiensMutation(s): 0 
Gene Names: POLR2APOLR2
EC: 2.7.7.6 (UniProt), 2.7.7.48 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24928 (Homo sapiens)
Explore P24928 
Go to UniProtKB:  P24928
PHAROS:  P24928
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24928
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.718α = 90
b = 46.923β = 92.3
c = 139.25γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references