4H3H

Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA poymerase II CTD peptide phosphorylated at SER-7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
SymplekinA, C [auth D]351Homo sapiensMutation(s): 0 
Gene Names: SYMPKSPK
Find proteins for Q92797 (Homo sapiens)
Explore Q92797 
Go to UniProtKB:  Q92797
NIH Common Fund Data Resources
PHAROS:  Q92797
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit A C-terminal domain phosphatase SSU72B, D [auth E]214Homo sapiensMutation(s): 1 
Gene Names: SSU72HSPC182PNAS-120
EC: 3.1.3.16
Find proteins for Q9NP77 (Homo sapiens)
Explore Q9NP77 
Go to UniProtKB:  Q9NP77
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PHAROS:  Q9NP77
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pol II CTD peptideE [auth F]10N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.819α = 90
b = 97.742β = 98.63
c = 104.603γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-09-13 
  • Released Date: 2012-10-31 
  • Deposition Author(s): Xiang, K., Tong, L.

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