9PSC | pdb_00009psc

Crystal structure of C. elegans PUF-3 in complex with pos-1 RNA mut1

• PDB DOI: https://doi.org/10.2210/pdb9PSC/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-07-25 Released: 2025-12-17 
• Deposition Author(s): Zhang, Y., Hall, T.M.T.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.244 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of C. elegans PUF-3 in complex with pos-1 RNA mut1

Zhang, Y., Hall, T.M.T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.79 kDa 
• Atom Count: 3,601 
• Modeled Residue Count: 419 
• Deposited Residue Count: 422 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUM-HD domain-containing protein	A	411	Caenorhabditis elegans	Mutation(s): 0  Gene Names: puf-3, CELE_Y45F10A.2, Y45F10A.2
UniProt
Find proteins for Q9U2G4 (Caenorhabditis elegans) Explore Q9U2G4  Go to UniProtKB:  Q9U2G4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
pos-1 RNA mut1	B	11	Caenorhabditis elegans

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.244 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.152	α = 90
b = 161.152	β = 90
c = 100.013	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Zhang, Y., Hall, T.M.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1ZIA-ES050165

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release