6N5Q

Structure of Human pir-miRNA-378a Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.946 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.0 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (128-MER)A128Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
2BA
Query on 2BA

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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
bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate
C20 H24 N10 O12 P2
PDXMFTWFFKBFIN-XPWFQUROSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
A
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.946 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.165 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 114.850α = 90.00
b = 114.850β = 90.00
c = 114.650γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1616265

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release