4ED5 | pdb_00004ed5

Crystal structure of the two N-terminal RRM domains of HuR complexed with RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.257 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4ED5

This is version 1.2 of the entry. See complete history

Literature

The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding.

Wang, H.Zeng, F.Liu, Q.Liu, H.Liu, Z.Niu, L.Teng, M.Li, X.

(2013) Acta Crystallogr D Biol Crystallogr 69: 373-380

  • DOI: https://doi.org/10.1107/S0907444912047828
  • Primary Citation Related Structures: 
    4ED5

  • PubMed Abstract: 

    Human RNA-binding protein (HuR), a ubiquitously expressed member of the Hu protein family, plays an important role in mRNA degradation and has been implicated as a key post-transcriptional regulator. HuR contains three RNA-recognition motif (RRM) domains. The two N-terminal tandem RRM domains can selectively bind AU-rich elements (AREs), while the third RRM domain (RRM3) contributes to interactions with the poly-A tail of target mRNA and other ligands. Here, the X-ray structure of two methylated tandem RRM domains (RRM1/2) of HuR in their RNA-free form was solved at 2.9 Å resolution. The crystal structure of RRM1/2 complexed with target mRNA was also solved at 2.0 Å resolution; comparisons of the two structures show that HuR RRM1/2 undergoes conformational changes upon RNA binding. Fluorescence polarization assays (FPA) were used to study the protein-RNA interactions. Both the structure and the FPA analysis indicated that RRM1 is the primary ARE-binding domain in HuR and that the conformational changes induce subsequent contacts of the RNA substrate with the inter-domain linker and RRM2 which greatly improve the RNA-binding affinity of HuR.


  • Organizational Affiliation
    • School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 47.27 kDa 
  • Atom Count: 3,220 
  • Modeled Residue Count: 357 
  • Deposited Residue Count: 376 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ELAV-like protein 1
A, B
177Homo sapiensMutation(s): 0 
Gene Names: ELAVL1HUR
UniProt & NIH Common Fund Data Resources
Find proteins for Q15717 (Homo sapiens)
Explore Q15717 
Go to UniProtKB:  Q15717
PHAROS:  Q15717
GTEx:  ENSG00000066044 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15717
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(*A*UP*UP*UP*UP*UP*AP*UP*UP*UP*U)-3'
C, D
11N/A
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M2M

Query on M2M



Download:Ideal Coordinates CCD File
J [auth A]1-METHOXY-2-(2-METHOXYETHOXY)ETHANE
C6 H14 O3
SBZXBUIDTXKZTM-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth D],
N [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.257 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.77α = 90
b = 62.75β = 111.89
c = 53.29γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations