2MKD

Human JAZ ZF3 Residues 168-227


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with favorable non-bond energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Characterization of Interactions between the Double-Stranded RNA-Binding Zinc Finger Protein JAZ and Nucleic Acids.

Burge, R.G.Martinez-Yamout, M.A.Dyson, H.J.Wright, P.E.

(2014) Biochemistry 53: 1495-1510

  • DOI: 10.1021/bi401675h
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The interactions of the human double-stranded RNA-binding zinc finger protein JAZ with RNA or DNA were investigated using electrophoretic mobility-shift assays, isothermal calorimetry, and nuclear magnetic resonance spectroscopy. Consistent with prev ...

    The interactions of the human double-stranded RNA-binding zinc finger protein JAZ with RNA or DNA were investigated using electrophoretic mobility-shift assays, isothermal calorimetry, and nuclear magnetic resonance spectroscopy. Consistent with previous reports, JAZ has very low affinity for duplex DNA or single-stranded RNA, but it binds preferentially to double-stranded RNA (dsRNA) with no detectable sequence specificity. The affinity of JAZ for dsRNA is unaffected by local structural features such as loops, overhangs, and bulges, provided a sufficient length of reasonably well-structured A-form RNA (about 18 bp for a single zinc finger) is present. Full-length JAZ contains four Cys2His2 zinc fingers (ZF1-4) and has the highest apparent affinity for dsRNA; two-finger constructs ZF12 and ZF23 have lower affinity, and ZF34 binds even more weakly. The fourth zinc finger, ZF4, has no measurable RNA-binding affinity. Single zinc finger constructs ZF1, ZF2, and ZF3 show evidence for multiple-site binding on the minimal RNA. Fitting of quantitative NMR titration and isothermal calorimetry data to a two-site binding model gave Kd1 ∼ 10 μM and Kd2 ∼ 100 μM. Models of JAZ-RNA complexes were generated using the high-ambiguity-driven biomolecular docking (HADDOCK) program. Single zinc fingers bind to the RNA backbone without sequence specificity, forming complexes with contacts between the RNA minor groove and residues in the N-terminal β strands and between the major groove and residues in the helix-kink-helix motif. We propose that the non-sequence-specific interaction between the zinc fingers of JAZ with dsRNA is dependent only on the overall shape of the A-form RNA.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc finger protein 346
A
60Homo sapiensMutation(s): 0 
Gene Names: ZNF346 (JAZ)
Find proteins for Q9UL40 (Homo sapiens)
Go to Gene View: ZNF346
Go to UniProtKB:  Q9UL40
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with favorable non-bond energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-03-26
    Type: Database references