9Q3F | pdb_00009q3f

Structure of neurodevelopmental mutant AGO1 F180del in complex with guide RNA

PDB DOI: https://doi.org/10.2210/pdb9Q3F/pdb
NAKB: 9Q3F
EM Map EMD-72192: EMDB EMDataResource

Classification: GENE REGULATION
Organism(s): Homo sapiens, Trichoplusia ni
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-08-18 Released: 2025-11-05
Deposition Author(s): Savidge, A., Adhav, V., Shen, Z., Fu, T., Nakanishi, K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of neurodevelopmental mutant AGO1 F180del in complex with guide RNA

Savidge, A., Zhang, H., Adhav, V., Kehling, A., Shen, Z., Fu, T., Nakanishi, K.

To be published.

Macromolecule Content

Total Structure Weight: 101.32 kDa
Atom Count: 6,615
Modeled Residue Count: 809
Deposited Residue Count: 878
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-1	A	870	Homo sapiens	Mutation(s): 0 Gene Names: AGO1, EIF2C1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL18 (Homo sapiens) Explore Q9UL18 Go to UniProtKB: Q9UL18
PHAROS: Q9UL18 GTEx: ENSG00000092847
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UL18
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Non-homogenous guide RNA	B	8	Trichoplusia ni
Sequence Annotations Expand
Reference Sequence

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	1.20.1_4487
RECONSTRUCTION	cryoSPARC	4.7.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.