9ZD5 | pdb_00009zd5

Human Stomatin - intramembrane region

PDB DOI: https://doi.org/10.2210/pdb9ZD5/pdb
EM Map EMD-74052: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2025-11-24 Released: 2026-03-04
Deposition Author(s): Vallese, F., Clarke, O.B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 91.6 kDa
Atom Count: 6,340
Modeled Residue Count: 776
Deposited Residue Count: 776
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stomatin	A [auth I], B [auth E], C [auth G], D [auth H]	194	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P27105 (Homo sapiens) Explore P27105 Go to UniProtKB: P27105
PHAROS: P27105 GTEx: ENSG00000148175
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27105
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLC (Subject of Investigation/LOI) Query on PLC Download:Ideal Coordinates CCD File SDF format, chain H [auth I] SDF format, chain M [auth E] SDF format, chain R [auth H] SDF format, chain S [auth H] MOL2 format, chain H [auth I] MOL2 format, chain M [auth E] MOL2 format, chain R [auth H] MOL2 format, chain S [auth H] mmCIF format, chain H [auth I] mmCIF format, chain M [auth E] mmCIF format, chain R [auth H] mmCIF format, chain S [auth H]	H [auth I], M [auth E], R [auth H], S [auth H]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain H [auth I] Focus chain M [auth E] Focus chain R [auth H] Focus chain S [auth H] Interactions & Density Focus chain H [auth I] Focus chain M [auth E] Focus chain R [auth H] Focus chain S [auth H]
S1P (Subject of Investigation/LOI) Query on S1P Download:Ideal Coordinates CCD File SDF format, chain I SDF format, chain N [auth E] SDF format, chain W [auth H] SDF format, chain X [auth H] MOL2 format, chain I MOL2 format, chain N [auth E] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] mmCIF format, chain I mmCIF format, chain N [auth E] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H]	I, N [auth E], W [auth H], X [auth H]	(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate C₁₈ H₃₈ N O₅ P DUYSYHSSBDVJSM-KRWOKUGFSA-N		Interactions Focus chain I Focus chain N [auth E] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain I Focus chain N [auth E] Focus chain W [auth H] Focus chain X [auth H]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain E [auth I] SDF format, chain F [auth I] SDF format, chain G [auth I] SDF format, chain J [auth E] SDF format, chain K [auth E] SDF format, chain L [auth E] SDF format, chain O [auth G] SDF format, chain P [auth G] SDF format, chain Q [auth G] SDF format, chain T [auth H] SDF format, chain U [auth H] SDF format, chain V [auth H] MOL2 format, chain E [auth I] MOL2 format, chain F [auth I] MOL2 format, chain G [auth I] MOL2 format, chain J [auth E] MOL2 format, chain K [auth E] MOL2 format, chain L [auth E] MOL2 format, chain O [auth G] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth H] MOL2 format, chain V [auth H] mmCIF format, chain E [auth I] mmCIF format, chain F [auth I] mmCIF format, chain G [auth I] mmCIF format, chain J [auth E] mmCIF format, chain K [auth E] mmCIF format, chain L [auth E] mmCIF format, chain O [auth G] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain T [auth H] mmCIF format, chain U [auth H] mmCIF format, chain V [auth H]	E [auth I] F [auth I] G [auth I] J [auth E] K [auth E] E [auth I], F [auth I], G [auth I], J [auth E], K [auth E], L [auth E], O [auth G], P [auth G], Q [auth G], T [auth H], U [auth H], V [auth H]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain E [auth I] Focus chain F [auth I] Focus chain G [auth I] Focus chain J [auth E] Focus chain K [auth E] Focus chain L [auth E] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Interactions & Density Focus chain E [auth I] Focus chain F [auth I] Focus chain G [auth I] Focus chain J [auth E] Focus chain K [auth E] Focus chain L [auth E] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H]