9YMD | pdb_00009ymd

Structure of AGO2 mature RISC (mat-RISC)

• PDB DOI: https://doi.org/10.2210/pdb9YMD/pdb
• EM Map EMD-73103: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2025-10-09 Released: 2026-06-03 
• Deposition Author(s): Zhang, H., Adhav, V.A., Kehling, A.C., Nakanishi, K.
• 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: 3.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structure of AGO2 mature RISC (mat-RISC)

Zhang, H., Adhav, V.A., Kehling, A.C., Nakanishi, K.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 105.18 kDa 
• Atom Count: 6,299 
• Modeled Residue Count: 769 
• Deposited Residue Count: 887 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-2	A	864	Homo sapiens	Mutation(s): 0  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
RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*AP*G)-3')	B	23	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v.4
MODEL REFINEMENT	PHENIX	1.21.2_5419
MODEL REFINEMENT	UCSF ChimeraX	1-6.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Zhang, H., Adhav, V.A., Kehling, A.C., Nakanishi, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM138997
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM124320

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release