9MUC | pdb_00009muc

Human IMPDH2 mutant - S160del, treated with GTP, ATP, IMP, and NAD+; interfacial octamer reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9MUC

This is version 1.1 of the entry. See complete history

Literature

An IMPDH2 variant associated with neurodevelopmental disorder disrupts purine biosynthesis and somite organization.

O'Neill, A.G.McCartney, M.E.Wheeler, G.M.Patel, J.H.Sanchez-Ramirez, G.Kollman, J.M.Wills, A.E.

(2025) Proc Natl Acad Sci U S A 122: e2511727122-e2511727122

  • DOI: https://doi.org/10.1073/pnas.2511727122
  • Primary Citation Related Structures: 
    9MUB, 9MUC

  • PubMed Abstract: 

    IMP dehydrogenase (IMPDH) controls a key regulatory node in purine biosynthesis. Gain-of-function mutations in human IMPDH2 are associated with neurodevelopmental disorders and neuromuscular symptoms including dystonia, but the developmental mechanisms underlying these defects are unknown. We previously showed that these mutants are insensitive to GTP inhibition and hypothesized that their hyperactivity would affect nucleotide metabolism in vivo. Here, we characterize the metabolic and developmental consequences of the neurodevelopmental disorder-associated IMPDH2 mutant, S160del, in Xenopus tropicalis . We show that expressing S160del but not WT human IMPDH2 disrupts purine pools and somite organization in the developing tadpole. We also show that S160del disrupts in vivo IMPDH filament assembly, a well-described IMPDH regulatory mechanism. Cryo-EM structures show that S160del disrupts filament assembly by destabilizing the dimerization of regulatory Bateman domains. Dimerization of Bateman domains and subsequent filament formation can be restored with a high affinity ligand, but this does not restore sensitivity to GTP inhibition, suggesting S160del also disrupts allostery of IMPDH2 filaments. This work demonstrates that the structural effects of patient IMPDH2 variants can cause disruptions both to nucleotide levels and to the normal development of sensorimotor structures, helping us better understand the physiological basis of disease in these patients.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195.

Macromolecule Content 

  • Total Structure Weight: 459.24 kDa 
  • Atom Count: 22,984 
  • Modeled Residue Count: 3,000 
  • Deposited Residue Count: 4,144 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase 2
A, B, C, D, E
A, B, C, D, E, F, G, H
518Homo sapiensMutation(s): 0 
Gene Names: IMPDH2IMPD2
EC: 1.1.1.205
UniProt & NIH Common Fund Data Resources
Find proteins for P12268 (Homo sapiens)
Explore P12268 
Go to UniProtKB:  P12268
PHAROS:  P12268
GTEx:  ENSG00000178035 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12268
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
(Subject of Investigation/LOI)

Query on NAD



Download:Ideal Coordinates CCD File
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
IMP
(Subject of Investigation/LOI)

Query on IMP



Download:Ideal Coordinates CCD File
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
W [auth H]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM149542
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008268

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2026-06-17
    Changes: Data collection, Database references