5T7B

Argonaute-2 - 5'-(E)-vinylphosphonate 2'-O-methyl-uridine modified mrTTR guide RNA complex

• PDB DOI: https://doi.org/10.2210/pdb5T7B/pdb
• NAKB: 5T7B

• Classification: HYDROLASE/RNA
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-09-02 Released: 2016-12-14 
• Deposition Author(s): Elkayam, E., Joshua-Tor, L.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.238 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Protein structure

Elkayam, E., Joshua-Tor, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104.4 kDa 
• Atom Count: 6,702 
• Modelled Residue Count: 813 
• Deposited Residue Count: 882 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-2	B [auth A]	861	Homo sapiens	Mutation(s): 2  Gene Names: AGO2, EIF2C2 EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV8 (Homo sapiens) Explore Q9UKV8  Go to UniProtKB:  Q9UKV8
PHAROS:  Q9UKV8 GTEx:  ENSG00000123908

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (UVP)UAUAGAGCAAGAACACUGUU	A [auth R]	21	Mus musculus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPH	C [auth A], D [auth A]	PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.238 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.207	α = 90
b = 108.306	β = 106.62
c = 68.821	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Elkayam, E., Joshua-Tor, L.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description