7ZJ4 | pdb_00007zj4

Ligand bound state of a brocolli-pepper aptamer FRET tile

• PDB DOI: https://doi.org/10.2210/pdb7ZJ4/pdb
• NAKB: 7ZJ4
• EM Map EMD-14740: EMDB EMDataResource

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2022-04-08 Released: 2023-04-19 
• Deposition Author(s): McRae, E.K.S., Vallina, N.S., Hansen, B.K., Boussebayle, A., Andersen, E.S.
• Funding Organization(s): Danish Council for Independent Research

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.43 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Structure determination of Pepper-Broccoli FRET pair by RNA origami scaffolding

McRae, E.K.S., Vallina, N.S., Hansen, B.K., Boussebayle, A., Andersen, E.S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 121.36 kDa 
• Atom Count: 8,026 
• Modeled Residue Count: 374 
• Deposited Residue Count: 374 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
brocolli-pepper aptamer	A [auth E]	374	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J93 (Subject of Investigation/LOI)	B [auth E]	4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]thieno[3,2-b]thiophen-2-yl]ethenyl]benzenecarbonitrile C19 H15 N3 O S2 RIGJCKIIBUZTCX-OVCLIPMQSA-N
1TU (Subject of Investigation/LOI)	C [auth E]	4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol C12 H12 F2 N2 O2 MSZRPLCUVKFQJC-UHFFFAOYSA-N
K	D [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.43 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	ISOLDE

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): McRae, E.K.S., Vallina, N.S., Hansen, B.K., Boussebayle, A., Andersen, E.S.

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Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	--

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Data collection, Refinement description