4L8R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.249 
  • R-Value Work: 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: 10.1126/science.1228705
  • Primary Citation of Related Structures:  4HXH

  • 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 t ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
3'-5' exoribonuclease 1
B, E
303Homo sapiensGene Names: ERI1 (3'EXO, THEX1)
EC: 3.1.-.-
Find proteins for Q8IV48 (Homo sapiens)
Go to Gene View: ERI1
Go to UniProtKB:  Q8IV48
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone RNA hairpin-binding protein
C
120Homo sapiensGene Names: SLBP (HBP)
Find proteins for Q14493 (Homo sapiens)
Go to Gene View: SLBP
Go to UniProtKB:  Q14493
Entity ID: 1
MoleculeChainsLengthOrganism
HISTONE MRNA STEM-LOOPA,D26N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.758α = 90.00
b = 90.802β = 90.00
c = 128.636γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CBASSdata collection
SnBphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-17 
  • Released Date: 2013-07-10 
  • Deposition Author(s): Tan, D., Tong, L.
  • This entry supersedes: 4HXH

Revision History 

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