9ZD0 | pdb_00009zd0

C3 local refinement of Urea Transporter B (SLC14A1) bound to human stomatin oligomer

• PDB DOI: https://doi.org/10.2210/pdb9ZD0/pdb
• EM Map EMD-74047: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-11-24 Released: 2026-02-25 
• Deposition Author(s): Vallese, F., Clarke, O.B.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Stomatin encapsulates aquaporin-1 and urea transporter-B in the erythrocyte membrane.

Vallese, F., Li, H., Barazzuol, L., Cali, T., Clarke, O.B.

(2026) Sci Adv 12: eaec1721-eaec1721

• PubMed: 41921000 
• DOI: https://doi.org/10.1126/sciadv.aec1721
• Primary Citation Related Structures: 
  9Z7U, 9ZCZ, 9ZD0, 9ZD2, 9ZD5


• PubMed Abstract: 
  

  Stomatin is a ubiquitous and highly expressed protein in erythrocytes, which associates with cholesterol-rich microdomains in the plasma membrane and is known to regulate the activity of multiple ion channels and transporters, but the structural basis of association with stomatin targets remains unknown. Here, we describe high-resolution structures of multiple stomatin complexes with endogenous binding partners isolated from human erythrocyte membranes, revealing that stomatin specifically associates with two membrane proteins involved in water transport and cell volume regulation, aquaporin-1 and the urea transporter SLC14A1. Together, our results reveal the structural basis of stomatin oligomerization, membrane association, and target recruitment and identify a putative role for stomatin in the regulation of osmotic balance in the erythrocyte.

---

Organizational Affiliation: 
• Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA.
Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA.
Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY 10032, USA.
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
Department of Biomedical Sciences, University of Padua, Padua, Italy.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 120.67 kDa 
• Atom Count: 8,355 
• Modeled Residue Count: 1,065 
• Deposited Residue Count: 1,065 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urea transporter 1	A, B, C	355	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13336 (Homo sapiens) Explore Q13336  Go to UniProtKB:  Q13336
PHAROS:  Q13336 GTEx:  ENSG00000141469

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTY	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Vallese, F., Clarke, O.B.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-02-25
  Type: Initial release
  
• Version 1.1: 2026-04-29
  Changes: Data collection, Database references