Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 74204.88 
• Atom Count: 5108 
• Residue Count: 523 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

6B3K

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

• DOI: 10.2210/pdb6B3K/pdb
• NDB: 6B3K

• Classification: immune system/rna
• Organism(s): synthetic construct
• Expression System: Escherichia coli, synthetic construct


• Deposited: 2017-09-22 Released: 2017-12-27 
• Deposition Author(s): DasGupta, S., Koirala, D., Shelke, S.A., Piccirilli, J.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Institute of General Medical Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 

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

• PubMed: 29309709 
• DOI: 10.1093/nar/gkx1292
• Primary Citation of Related Structures:  
  6B14


• 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. 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.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Heavy chain of Fab BL3-6	H	225	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Light chain of Fab BL3-6	L	215	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Length	Organism
RNA (83-MER),RNA (83-MER)	R	83	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	L	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 147.216	α = 90.00
b = 80.019	β = 111.47
c = 93.405	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PHENIX	phasing
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-09-22 
• Released Date: 2017-12-27 
• Deposition Author(s): DasGupta, S., Koirala, D., Shelke, S.A., Piccirilli, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	R01AI081987
National Institutes of Health/National Institute of General Medical Sciences	United States	R01GM102489

Revision History 

• Version 1.0: 2017-12-27
  Type: Initial release
• Version 1.1: 2018-01-17
  Type: Author supporting evidence, Database references, Structure summary
• Version 1.2: 2018-01-24
  Type: Database references
• Version 1.3: 2018-04-04
  Type: Data collection, Database references