9C7A

Crystal structure of R149W neurodevelopmental disease-associated U2AF2 variant

• PDB DOI: https://doi.org/10.2210/pdb9C7A/pdb

• Classification: RNA BINDING PROTEIN/RNA/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2024-06-10 Released: 2024-10-02 
• Deposition Author(s): Maji, D., Jenkins, J.L., Kielkopf, C.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.159 
• R-Value Work: 0.130 
• R-Value Observed: 0.132 

Starting Model: experimental

Literature

Recurrent neurodevelopmentally-associated variants of the pre-mRNA splicing factor U2AF2 alter RNA binding affinities and interactions

Maji, D., Jenkins, J.L., Boutz, P.L., Kielkopf, C.L.

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: homology

Macromolecule Content

• Total Structure Weight: 24.85 kDa 
• Atom Count: 1,987 
• Modelled Residue Count: 204 
• Deposited Residue Count: 212 
• Unique protein chains: 1
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor U2AF 65 kDa subunit	A	204	Homo sapiens	Mutation(s): 1  Gene Names: U2AF2, U2AF65
UniProt & NIH Common Fund Data Resources
Find proteins for P26368 (Homo sapiens) Explore P26368  Go to UniProtKB:  P26368
PHAROS:  P26368 GTEx:  ENSG00000063244

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(P*UP*U)-D(P*U)-R(P*UP*U)-D(P*(BRU))-R(P*CP*C)-3')	B	8	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.159 
• R-Value Work: 0.130 
• R-Value Observed: 0.132 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.25	α = 90
b = 63.131	β = 90
c = 77.559	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Maji, D., Jenkins, J.L., Kielkopf, C.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM070503-15

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release