9OTN | pdb_00009otn

Human glutamine synthetase filament bound to ATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.11 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity.

Greene, E.Muniz, R.Yamamura, H.Hoff, S.E.Bajaj, P.Lee, D.J.Thompson, E.M.Arada, A.Lee, G.M.Bonomi, M.Kollman, J.M.Fraser, J.S.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.07.04.663231
  • Primary Citation of Related Structures:  
    9OTM, 9OTN, 9OTO, 9OTP, 9OTQ

  • PubMed Abstract: 

    To maintain metabolic homeostasis, enzymes must adapt to fluctuating nutrient levels through mechanisms beyond gene expression. Here, we demonstrate that human glutamine synthetase (GS) can reversibly polymerize into filaments aided by a composite binding site formed at the filament interface by the product, glutamine. Time-resolved cryo-electron microscopy (cryo-EM) confirms that glutamine binding stabilizes these filaments, which in turn exhibit reduced catalytic specificity for ammonia at physiological concentrations. This inhibition appears induced by a conformational change that remodulates the active site loop ensemble gating substrate entry. Metadynamics ensemble refinement revealed >10 Å conformational range for the active site loop and that the loop is stabilized by transient contacts. This disorder is significant, as we show that the transient contacts which stabilize this loop in a closed conformation are essential for catalysis both in vitro and in cells. We propose that GS filament formation constitutes a negative-feedback mechanism, directly linking product concentration to the structural and functional remodeling of the enzyme.


  • Organizational Affiliation
    • Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine synthetase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
373Homo sapiensMutation(s): 0 
Gene Names: GLULGLNS
EC: 6.3.1.2 (PDB Primary Data), 2.3.1.225 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P15104 (Homo sapiens)
Explore P15104 
Go to UniProtKB:  P15104
PHAROS:  P15104
GTEx:  ENSG00000135821 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15104
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth C]
BB [auth L]
BC [auth T]
DA [auth D]
GA [auth E]
AA [auth C],
BB [auth L],
BC [auth T],
DA [auth D],
GA [auth E],
GB [auth M],
HB [auth N],
JA [auth F],
KB [auth O],
NB [auth P],
OA [auth G],
PA [auth H],
SA [auth I],
SB [auth Q],
TB [auth R],
U [auth A],
X [auth B],
XA [auth J],
XB [auth S],
YA [auth K]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AB [auth K]
AC [auth T]
BA [auth C]
CA [auth C]
CB [auth L]
AB [auth K],
AC [auth T],
BA [auth C],
CA [auth C],
CB [auth L],
DB [auth L],
EA [auth D],
EB [auth M],
FA [auth D],
FB [auth M],
HA [auth E],
IA [auth E],
IB [auth N],
JB [auth N],
KA [auth F],
LA [auth F],
LB [auth O],
MA [auth G],
MB [auth O],
NA [auth G],
OB [auth P],
PB [auth P],
QA [auth H],
QB [auth Q],
RA [auth H],
RB [auth Q],
TA [auth I],
UA [auth I],
UB [auth R],
V [auth A],
VA [auth J],
VB [auth R],
W [auth A],
WA [auth J],
WB [auth S],
Y [auth B],
YB [auth S],
Z [auth B],
ZA [auth K],
ZB [auth T]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.11 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

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 States1F32GM144981-01
Human Frontier Science Program (HFSP)FranceRGP0054
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM123159
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM145238

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Database references