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

  • 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 phosphorylated at four serines in its 18-aa C-terminal tail ...

    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

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
3'-5' exoribonuclease 1
B, E
303Homo sapiensMutation(s): 0 
Gene Names: ERI1, 3'EXO, THEX1
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IV48 (Homo sapiens)
Explore Q8IV48 
Go to UniProtKB:  Q8IV48
PHAROS:  Q8IV48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IV48
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone RNA hairpin-binding protein120Homo sapiensMutation(s): 0 
Gene Names: SLBP, HBP
UniProt & NIH Common Fund Data Resources
Find proteins for Q14493 (Homo sapiens)
Explore Q14493 
Go to UniProtKB:  Q14493
PHAROS:  Q14493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14493
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
histone mRNA stem-loop
A, D
26N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
C
L-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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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