4L8R

Structure of mrna stem-loop, human stem-loop binding protein and 3'hexo ternary complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structure of Histone Mrna Stem-Loop, Human Stem-Loop Binding Protein, and 3'Hexo Ternary Complex.

Tan, D., Marzluff, W.F., Dominski, Z., Tong, L.

(2013) Science 339: 318

  • DOI: https://doi.org/10.1126/science.1228705
  • Primary Citation of Related Structures:  
    4L8R

  • PubMed Abstract: 

    Metazoan replication-dependent histone messenger RNAs (mRNAs) have a conserved stem-loop (SL) at their 3'-end. The stem-loop binding protein (SLBP) specifically recognizes the SL to regulate histone mRNA metabolism, and the 3'-5' exonuclease 3'hExo trims its 3'-end after processing. We report the crystal structure of a ternary complex of human SLBP RNA binding domain, human 3'hExo, and a 26-nucleotide SL RNA. Only one base of the SL is recognized specifically by SLBP, and the two proteins primarily recognize the shape of the RNA. SLBP and 3'hExo have no direct contact with each other, and induced structural changes in the loop of the SL mediate their cooperative binding. The 3' flanking sequence is positioned in the 3'hExo active site, but the ternary complex limits the extent of trimming.

    • Organizational Affiliation: 

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3'-5' exoribonuclease 1
B, E
303Homo sapiensMutation(s): 0 
Gene Names: 3'EXO, ERI1, THEX1
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IV48 (Homo sapiens)
Explore Q8IV48 
Go to UniProtKB:  Q8IV48
PHAROS:  Q8IV48
GTEx:  ENSG00000104626 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IV48
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone RNA hairpin-binding protein120Homo sapiensMutation(s): 0 
Gene Names: HBP, SLBP
UniProt & NIH Common Fund Data Resources
Find proteins for Q14493 (Homo sapiens)
Explore Q14493 
Go to UniProtKB:  Q14493
PHAROS:  Q14493
GTEx:  ENSG00000163950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14493
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
HISTONE MRNA STEM-LOOP
A, D
26N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
B, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.758α = 90
b = 90.802β = 90
c = 128.636γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
SnBphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2013-07-10 
    • Deposition Author(s): Tan, D., Tong, L.
  • This entry supersedes: 4HXH

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description