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- PDB-9zd2: C1 local refinement of aquaporin 1 bound to endogenous human stomatin -

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Basic information

Entry
Database: PDB / ID: 9zd2
TitleC1 local refinement of aquaporin 1 bound to endogenous human stomatin
Components
  • Aquaporin-1
  • Stomatin
KeywordsMEMBRANE PROTEIN / Oligomer / C8 symmetry / scaffold
Function / homology
Function and homology information


metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / nitric oxide transmembrane transporter activity / hydrogen peroxide channel activity / lipid digestion / renal water transport / corticotropin secretion / cellular response to salt stress ...metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / nitric oxide transmembrane transporter activity / hydrogen peroxide channel activity / lipid digestion / renal water transport / corticotropin secretion / cellular response to salt stress / positive regulation of viral process / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / glycerol transmembrane transporter activity / secretory granule organization / water transmembrane transporter activity / cerebrospinal fluid secretion / positive regulation of saliva secretion / Passive transport by Aquaporins / pancreatic juice secretion / establishment or maintenance of actin cytoskeleton polarity / lateral ventricle development / glycerol transmembrane transport / cellular response to mercury ion / intracellular water homeostasis / intracellularly cGMP-activated cation channel activity / renal water absorption / potassium ion transmembrane transporter activity / transepithelial water transport / host-mediated activation of viral genome replication / water channel activity / ammonium transmembrane transport / ammonium channel activity / ankyrin-1 complex / glomerular filtration / camera-type eye morphogenesis / fibroblast migration / multicellular organismal-level water homeostasis / water transport / cellular hyperosmotic response / cellular homeostasis / regulation of monoatomic ion transmembrane transport / cell volume homeostasis / RNA polymerase binding / hyperosmotic response / positive regulation of fibroblast migration / odontogenesis / nitric oxide transport / 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 / brush border / RHOH GTPase cycle / RHOA GTPase cycle / cellular response to dexamethasone stimulus / positive regulation of protein targeting to membrane / potassium channel activity / transmembrane transporter activity / specific granule membrane / renal water homeostasis / ephrin receptor binding / cellular response to retinoic acid / cellular response to nitric oxide / sensory perception of pain / establishment of localization in cell / basal plasma membrane / cellular response to copper ion / cellular response to cAMP / Developmental Lineage of Pancreatic Ductal Cells / carbon dioxide transport / potassium ion transport / wound healing / brush border membrane / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / cellular response to mechanical stimulus / sarcolemma / Stimuli-sensing channels / positive regulation of fibroblast proliferation / cellular response to hydrogen peroxide / positive regulation of angiogenesis / apical part of cell / cellular response to UV / melanosome / Vasopressin regulates renal water homeostasis via Aquaporins / blood microparticle / nuclear membrane / cellular response to hypoxia / vesicle / defense response to Gram-negative bacterium / basolateral plasma membrane / cytoskeleton / apical plasma membrane / membrane raft / axon
Similarity search - Function
Aquaporin 1 / 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 / Aquaporin transporter / Major intrinsic protein, conserved site ...Aquaporin 1 / 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 / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Band 7/SPFH domain superfamily / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
CHOLESTEROL / PALMITIC ACID / Stomatin / Aquaporin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Aquaporin-1
B: Aquaporin-1
C: Aquaporin-1
A: Aquaporin-1
F: Stomatin
G: Stomatin
E: Stomatin
I: Stomatin
H: Stomatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,20017
Polymers209,6289
Non-polymers2,5728
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
Aquaporin-1 / AQP-1 / Aquaporin-CHIP / Channel-like integral membrane protein of 28 kDa / Urine water channel


Mass: 25996.072 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Aquaporin-1 / Source: (natural) Homo sapiens (human) / References: UniProt: P29972
#2: Protein
Stomatin / Erythrocyte band 7 integral membrane protein / Erythrocyte membrane protein band 7.2 / Protein 7.2b


Mass: 21128.730 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: Stomatin region in contact with AQP-1,Stomatin region in contact with AQP-1
Source: (natural) Homo sapiens (human) / References: UniProt: P27105
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H32O2 / Details: Aquaporin-1 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C27H46O / 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: The stomatin region in contact with two AQP-1 monomers
Type: COMPLEX / Entity ID: #1-#2 / 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
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415075
ELECTRON MICROSCOPYf_angle_d0.68220522
ELECTRON MICROSCOPYf_dihedral_angle_d6.7842400
ELECTRON MICROSCOPYf_chiral_restr0.0452508
ELECTRON MICROSCOPYf_plane_restr0.0042542

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