6ROL

Structure of IMP2 KH34 domains

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

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: 10.1038/s41467-019-12193-7
  • Primary Citation of Related Structures:  
    6ROL

  • 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 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 Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. carolina.eliscovich@einstein.yu.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin-like growth factor 2 mRNA-binding protein 2A, B, C, D166Homo sapiensMutation(s): 0 
Gene Names: IGF2BP2, IMP2, VICKZ2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6M1 (Homo sapiens)
Explore Q9Y6M1 
Go to UniProtKB:  Q9Y6M1
PHAROS:  Q9Y6M1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6M1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
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]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
CA [auth C],
DA [auth C],
L [auth A],
M [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
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]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
iMOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

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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