4H3K

Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA polymerase II CTD peptide phosphorylated at Ser-2, Ser-5 and Ser-7

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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This is version 1.2 of the entry. See complete history. 


Literature

An unexpected binding mode for a Pol II CTD peptide phosphorylated at Ser7 in the active site of the CTD phosphatase Ssu72.

Xiang, K., Manley, J.L., Tong, L.

(2012) Genes Dev 26: 2265-2270

  • DOI: https://doi.org/10.1101/gad.198853.112
  • Primary Citation of Related Structures:  
    4H3H, 4H3K

  • PubMed Abstract: 

    Ssu72, an RNA polymerase II C-terminal domain (CTD) phospho-Ser5 (pSer5) phosphatase, was recently reported to have pSer7 phosphatase activity as well. We report here the crystal structure of a ternary complex of the N-terminal domain of human symplekin, human Ssu72, and a 10-mer pSer7 CTD peptide. Surprisingly, the peptide is bound in the Ssu72 active site with its backbone running in the opposite direction compared with a pSer5 peptide. The pSer7 phosphatase activity of Ssu72 is ∼4000-fold lower than its pSer5 phosphatase activity toward a peptide substrate, consistent with the structural observations.

    • Organizational Affiliation: 

    Department of Biological Sciences, Columbia University, New York, New York 10027, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SymplekinA,
C [auth D]		351Homo sapiensMutation(s): 0 
Gene Names: SYMPK, SPK
UniProt & NIH Common Fund Data Resources
Find proteins for Q92797 (Homo sapiens)
Explore Q92797 
Go to UniProtKB:  Q92797
PHAROS:  Q92797
GTEx:  ENSG00000125755 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92797
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit A C-terminal domain phosphatase SSU72B,
D [auth E]		214Homo sapiensMutation(s): 1 
Gene Names: SSU72, HSPC182, PNAS-120
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP77 (Homo sapiens)
Explore Q9NP77 
Go to UniProtKB:  Q9NP77
PHAROS:  Q9NP77
GTEx:  ENSG00000160075 
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UniProt GroupQ9NP77
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HexapeptideE [auth F]10N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
F [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP		E [auth F]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.583α = 90
b = 97.364β = 97.86
c = 105.278γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary