9CMP | pdb_00009cmp

Structure of human Argonaute2-guide-target complex in a fully paired, slicing-competent conformation

• PDB DOI: https://doi.org/10.2210/pdb9CMP/pdb
• EM Map EMD-45752: EMDB EMDataResource
• NAKB: 9CMP

• Classification: HYDROLASE/RNA
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-07-15 Released: 2024-12-11 
• Deposition Author(s): Mohamed, A.A., Wang, P.Y., Bartel, D.P., Vos, S.M.
• 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: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The structural basis for RNA slicing by human Argonaute2.

Mohamed, A.A., Wang, P.Y., Bartel, D.P., Vos, S.M.

(2025) Cell Rep 44: 115166-115166

• PubMed: 39932188 
• DOI: https://doi.org/10.1016/j.celrep.2024.115166
• Primary Citation Related Structures: 
  9CMP


• PubMed Abstract: 
  

  Argonaute (AGO) proteins associate with guide RNAs to form complexes that slice transcripts that pair to the guide. This slicing drives post-transcriptional gene silencing through RNA interference (RNAi), which is essential for many eukaryotes and the basis for new clinical therapies. Despite this importance, structural information on eukaryotic AGOs in a fully paired, slicing-competent conformation-hypothesized to be intrinsically unstable-has been lacking. Here, we present the cryogenic electron microscopy structure of a human AGO-guide complex bound to a fully paired target, revealing structural rearrangements that enable this conformation. Critically, the N domain of AGO rotates to allow the RNA full access to the central channel and forms contacts that license rapid slicing. Moreover, a conserved loop in the PIWI domain secures the RNA near the active site to enhance slicing rate and specificity. These results explain how AGO accommodates targets possessing pairing specificity typically observed in biological and clinical slicing substrates.

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Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA.
Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA.
Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA. Electronic address: [e-mail].
Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA. Electronic address: [e-mail].

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: 113.23 kDa 
• Atom Count: 6,211 
• Modeled Residue Count: 811 
• Deposited Residue Count: 910 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-2	C [auth A]	860	Homo sapiens	Mutation(s): 1  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 (5'-R(P*UP*GP*GP*AP*AP*GP*AP*CP*UP*AP*GP*UP*GP*AP*UP*UP*UP*UP*GP*UP*U)-3')	A [auth G]	22	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*AP*AP*CP*AP*AP*AP*AP*UP*CP*AP*CP*UP*AP*GP*UP*CP*UP*UP*CP*CP*A)-3')	B [auth T]	28	Homo sapiens

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Mohamed, A.A., Wang, P.Y., Bartel, D.P., Vos, S.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2 GM146254

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2025-01-08
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-02-26
  Changes: Data collection, Database references
• Version 1.3: 2025-05-14
  Changes: Data collection