4QOZ

Crystal structure of the histone mRNA stem-loop, stem-loop binding protein (phosphorylated), and 3'hExo ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation.

Zhang, J.Tan, D.DeRose, E.F.Perera, L.Dominski, Z.Marzluff, W.F.Tong, L.Hall, T.M.

(2014) Proc Natl Acad Sci U S A 111: E2937-E2946

  • DOI: 10.1073/pnas.1406381111
  • Primary Citation of Related Structures:  
    4QOZ, 4TV0, 4TUW, 4TUX

  • PubMed Abstract: 
  • Replication-dependent histone mRNAs end with a conserved stem loop that is recognized by stem-loop-binding protein (SLBP). The minimal RNA-processing domain of SLBP is phosphorylated at an internal threonine, and Drosophila SLBP (dSLBP) also is phosp ...

    Replication-dependent histone mRNAs end with a conserved stem loop that is recognized by stem-loop-binding protein (SLBP). The minimal RNA-processing domain of SLBP is phosphorylated at an internal threonine, and Drosophila SLBP (dSLBP) also is phosphorylated at four serines in its 18-aa C-terminal tail. We show that phosphorylation of dSLBP increases RNA-binding affinity dramatically, and we use structural and biophysical analyses of dSLBP and a crystal structure of human SLBP phosphorylated on the internal threonine to understand the striking improvement in RNA binding. Together these results suggest that, although the C-terminal tail of dSLBP does not contact the RNA, phosphorylation of the tail promotes SLBP conformations competent for RNA binding and thereby appears to reduce the entropic penalty for the association. Increased negative charge in this C-terminal tail balances positively charged residues, allowing a more compact ensemble of structures in the absence of RNA.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; marzluff@med.unc.edu ltong@columbia.edu hall4@niehs.nih.gov.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
3'-5' exoribonuclease 1BE303Homo sapiensMutation(s): 0 
Gene Names: ERI13'EXOTHEX1
EC: 3.1
Find proteins for Q8IV48 (Homo sapiens)
Explore Q8IV48 
Go to UniProtKB:  Q8IV48
NIH Common Fund Data Resources
PHAROS  Q8IV48
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone RNA hairpin-binding proteinC120Homo sapiensMutation(s): 0 
Gene Names: SLBPHBP
Find proteins for Q14493 (Homo sapiens)
Explore Q14493 
Go to UniProtKB:  Q14493
NIH Common Fund Data Resources
PHAROS  Q14493
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
histone mRNA stem-loopA, D26N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
CL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.107α = 90
b = 91.505β = 90
c = 128.722γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
COMOphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-06-21 
  • Released Date: 2014-07-23 
  • Deposition Author(s): Tan, D., Tong, L.

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-08-06
    Changes: Database references