6DB8

Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86541 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.

Shelke, S.A.Shao, Y.Laski, A.Koirala, D.Weissman, B.P.Fuller, J.R.Tan, X.Constantin, T.P.Waggoner, A.S.Bruchez, M.P.Armitage, B.A.Piccirilli, J.A.

(2018) Nat Commun 9: 4542-4542


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab-Heavy chain
H
232N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab-Light chain
L
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (60-MER)R60synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4A
Query on G4A

Download SDF File 
Download CCD File 
R
2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium
C19 H19 N2 O4 S2
AHPYSIGATYXERL-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86541 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.219 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 109.158α = 90.00
b = 118.442β = 90.00
c = 119.310γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01AI081987

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release