Structure of IMP2 KH34 domains

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.198 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


The structural basis for RNA selectivity by the IMP family of RNA-binding proteins.

Biswas, J.Patel, V.L.Bhaskar, V.Chao, J.A.Singer, R.H.Eliscovich, C.

(2019) Nat Commun 10: 4440-4440

  • DOI: https://doi.org/10.1038/s41467-019-12193-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The IGF2 mRNA-binding proteins (ZBP1/IMP1, IMP2, IMP3) are highly conserved post-transcriptional regulators of RNA stability, localization and translation. They play important roles in cell migration, neural development, metabolism and cancer cell survival. The knockout phenotypes of individual IMP proteins suggest that each family member regulates a unique pool of RNAs, yet evidence and an underlying mechanism for this is lacking. Here, we combine systematic evolution of ligands by exponential enrichment (SELEX) and NMR spectroscopy to demonstrate that the major RNA-binding domains of the two most distantly related IMPs (ZBP1 and IMP2) bind to different consensus sequences and regulate targets consistent with their knockout phenotypes and roles in disease. We find that the targeting specificity of each IMP is determined by few amino acids in their variable loops. As variable loops often differ amongst KH domain paralogs, we hypothesize that this is a general mechanism for evolving specificity and regulation of the transcriptome.

  • Organizational Affiliation

    Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. robert.singer@einstein.yu.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin-like growth factor 2 mRNA-binding protein 2
A, B, C, D
166Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6M1 (Homo sapiens)
Explore Q9Y6M1 
Go to UniProtKB:  Q9Y6M1
GTEx:  ENSG00000073792 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6M1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
HA [auth D]
IA [auth D]
JA [auth D]
AA [auth C],
BA [auth C],
HA [auth D],
IA [auth D],
JA [auth D],
K [auth A],
P [auth B],
X [auth C],
Y [auth C],
Z [auth C]
C4 H10 O3
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth C],
DA [auth C],
L [auth A],
M [auth A]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
EA [auth D]
F [auth A]
FA [auth D]
G [auth A]
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.88α = 90
b = 62.38β = 91.32
c = 85.74γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_156477

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description