6N5S | pdb_00006n5s

Structure of Human pir-miRNA-320b-2 Apical Loop and One-base-pair Stem Fused to the YdaO Riboswitch Scaffold

PDB DOI: https://doi.org/10.2210/pdb6N5S/pdb
NAKB: 6N5S

Classification: RNA
Organism(s): Homo sapiens
Expression System: in vitro transcription vector pT7-Fluc(deltai)
Mutation(s): No

Deposited: 2018-11-22 Released: 2019-11-27
Deposition Author(s): Shoffner, G.M., Peng, Z., Guo, F.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.201 (Depositor), 0.208 (DCC)
R-Value Work:
0.176 (Depositor), 0.189 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Three-dimensional structures of pri-miRNA apical junctions and loops revealed by scaffold-directed crystallography

Shoffner, G.M., Peng, Z., Guo, F.

To be published.

Macromolecule Content

Total Structure Weight: 41.86 kDa
Atom Count: 2,768
Modeled Residue Count: 123
Deposited Residue Count: 123
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (123-MER)	A	123	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2BA Query on 2BA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide C₂₀ H₂₄ N₁₀ O₁₂ P₂ PDXMFTWFFKBFIN-XPWFQUROSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
5GP Query on 5GP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A]	E [auth A], F [auth A], H [auth A], I [auth A], K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.201 (Depositor), 0.208 (DCC)
R-Value Work: 0.176 (Depositor), 0.189 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.56	α = 90
b = 114.56	β = 90
c = 115.06	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Shoffner, G.M.

Peng, Z.

Guo, F.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1616265

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.0: 2024-10-16
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary