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- PDB-9zd5: Human Stomatin - intramembrane region -

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Basic information

Entry
Database: PDB / ID: 9zd5
TitleHuman Stomatin - intramembrane region
ComponentsStomatin
KeywordsMEMBRANE PROTEIN / Oligomer / C8 symmetry / scaffold / intramembrane region
Function / homology
Function and homology information


positive regulation of viral process / host-mediated activation of viral genome replication / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / azurophil granule membrane / RHOB GTPase cycle / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / ion channel inhibitor activity ...positive regulation of viral process / host-mediated activation of viral genome replication / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / azurophil granule membrane / RHOB GTPase cycle / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / ion channel inhibitor activity / CDC42 GTPase cycle / tertiary granule membrane / RHOH GTPase cycle / RHOA GTPase cycle / positive regulation of protein targeting to membrane / specific granule membrane / Stimuli-sensing channels / melanosome / blood microparticle / vesicle / cytoskeleton / membrane raft / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / mitochondrion / : / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Band-7 stomatin-like / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
DIUNDECYL PHOSPHATIDYL CHOLINE / PALMITIC ACID / Chem-S1P / Stomatin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsVallese, F. / Clarke, O.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2026
Title: Stomatin encapsulates aquaporin-1 and urea transporter-B in the erythrocyte membrane.
Authors: Francesca Vallese / Huan Li / Lucia Barazzuol / Tito Calì / Oliver B Clarke /
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 ...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.
History
DepositionNov 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
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Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Stomatin
E: Stomatin
G: Stomatin
H: Stomatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,60124
Polymers84,5154
Non-polymers7,08620
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Stomatin / Erythrocyte band 7 integral membrane protein / Erythrocyte membrane protein band 7.2 / Protein 7.2b


Mass: 21128.730 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27105
#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C16H32O2
#3: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H65NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: Chemical
ChemComp-S1P / (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate / sphingosine 1-phosphate


Mass: 379.472 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H38NO5P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Stomatin oligomer formed by 16 subunits with C8 symmetry.
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2151648 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036428
ELECTRON MICROSCOPYf_angle_d0.6048628
ELECTRON MICROSCOPYf_dihedral_angle_d17.8421220
ELECTRON MICROSCOPYf_chiral_restr0.0491008
ELECTRON MICROSCOPYf_plane_restr0.0031024

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