6B14

Crystal structure of Spinach RNA aptamer in complex with Fab BL3-6S97N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography.

Koirala, D.Shelke, S.A.Dupont, M.Ruiz, S.DasGupta, S.Bailey, L.J.Benner, S.A.Piccirilli, J.A.

(2018) Nucleic Acids Res 46: 2624-2635

  • DOI: 10.1093/nar/gkx1292
  • Primary Citation of Related Structures:  
    6B14, 6B3K

  • PubMed Abstract: 
  • Antibody fragments such as Fabs possess properties that can enhance protein and RNA crystallization and therefore can facilitate macromolecular structure determination. In particular, Fab BL3-6 binds to an AAACA RNA pentaloop closed by a GC pair with ∼100 nM affinity ...

    Antibody fragments such as Fabs possess properties that can enhance protein and RNA crystallization and therefore can facilitate macromolecular structure determination. In particular, Fab BL3-6 binds to an AAACA RNA pentaloop closed by a GC pair with ∼100 nM affinity. The Fab and hairpin have served as a portable module for RNA crystallization. The potential for general application make it desirable to adjust the properties of this crystallization module in a manner that facilitates its use for RNA structure determination, such as ease of purification, surface entropy or binding affinity. In this work, we used both in vitro RNA selection and phage display selection to alter the epitope and paratope sides of the binding interface, respectively, for improved binding affinity. We identified a 5'-GNGACCC-3' consensus motif in the RNA and S97N mutation in complimentarity determining region L3 of the Fab that independently impart about an order of magnitude improvement in affinity, resulting from new hydrogen bonding interactions. Using a model RNA, these modifications facilitated crystallization under a wider range of conditions and improved diffraction. The improved features of the Fab-RNA module may facilitate its use as an affinity tag for RNA purification and imaging and as a chaperone for RNA crystallography.


    Organizational Affiliation

    Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy chain of Fab BL3-6S97N H225Mus musculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Light chain of Fab BL3-6S97N L215Mus musculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (86-MER)R83synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.773α = 90
b = 79.993β = 111.76
c = 92.892γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM102489
Defense Threat Reduction Agency (DTRA)United StatesHDTRA1-13-1-0004

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Source and taxonomy
  • Version 1.2: 2018-01-17
    Changes: Author supporting evidence, Database references, Structure summary
  • Version 1.3: 2018-01-24
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.5: 2018-04-11
    Changes: Data collection, Source and taxonomy
  • Version 1.6: 2020-01-01
    Changes: Author supporting evidence