8RDD

Crystal structure of Saccharomyces cerevisiae Nmd4 protein involved in nonsense mediated mRNA decay

• PDB DOI: https://doi.org/10.2210/pdb8RDD/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-08 Released: 2024-08-14 
• Deposition Author(s): Barbarin-Bocahu, I., Graille, M.
• Funding Organization(s): Agence Nationale de la Recherche (ANR), Centre National de la Recherche Scientifique (CNRS), Ecole polytechnique

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.192 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Structure of a yeast protein

Barbarin-Bocahu, I., Ulryck, N., Rigobert, A., Ruiz Gutierrez, N., Decourty, L., Raji, M., Garkhal, B., Le Hir, H., Saveanu, C., Graille, M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 19.84 kDa 
• Atom Count: 1,583 
• Modelled Residue Count: 164 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nonsense-mediated decay protein 4	A [auth B]	170	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NMD4
UniProt
Find proteins for Q12129 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12129  Go to UniProtKB:  Q12129

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	C [auth B], D [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A [auth B]	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.192 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.371	α = 90
b = 80.371	β = 90
c = 94.134	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Barbarin-Bocahu, I., Graille, M.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-18-CE11-0003-04
Centre National de la Recherche Scientifique (CNRS)	France	--
Ecole polytechnique	France	--

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release