9DHX | pdb_00009dhx

human Argonaute2 R315V/H316A - guide RNA in complex with a fully complementary target

• PDB DOI: https://doi.org/10.2210/pdb9DHX/pdb
• NAKB: 9DHX
• EM Map EMD-46888: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-09-04 Released: 2026-03-04 
• Deposition Author(s): Sarkar, S., Gebert, L.F.R., MacRae, I.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

human Argonaute2 R315V/H316A - miR-122 in complex with a fully complementary target

Sarkar, S., Gebert, L.F.R., MacRae, I.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 110.38 kDa 
• Atom Count: 6,318 
• Modeled Residue Count: 725 
• Deposited Residue Count: 900 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Argonaute2 R315V/H316A	A	859	Homo sapiens	Mutation(s): 7  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: 2
Molecule	Chains	Length	Organism	Image
guide RNA	B	20	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
target RNA	C	21	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.3
MODEL REFINEMENT	PHENIX	1.20.1
MODEL REFINEMENT	Coot	0.9.8.1
MODEL REFINEMENT	UCSF ChimeraX	1.7.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-04 
Deposition Author(s): Sarkar, S., Gebert, L.F.R., MacRae, I.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R35GM127090

Revision History  

• Version 1.0: 2026-03-04
  Type: Initial release
  
• Version 1.1: 2026-03-11
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2026-05-13
  Changes: Data collection, Structure summary