7ZJ5 | pdb_00007zj5

Unbound state of a brocolli-pepper aptamer FRET tile.

PDB DOI: https://doi.org/10.2210/pdb7ZJ5/pdb
EM Map EMD-14741: EMDB EMDataResource
NAKB: 7ZJ5

Classification: RNA
Organism(s): synthetic construct
Expression System: 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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.55 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7ZJ5

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 120.74 kDa
Atom Count: 7,984
Modeled Residue Count: 374
Deposited Residue Count: 374
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff)

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download:Ideal Coordinates CCD File SDF format, chain B [auth E] MOL2 format, chain B [auth E] mmCIF format, chain B [auth E]	B [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth E] Interactions & Density Focus chain B [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.55 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-19

Deposition Author(s):

Boussebayle, A.

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

Revision History (Full details and data files)

Version 1.0: 2023-04-19
Type: Initial release
Version 1.1: 2023-05-24
Changes: Structure summary
Version 1.2: 2023-07-26
Changes: Other
Version 1.3: 2024-07-24
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.