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- PDB-9zcz: C4 local refinement of stomatin-bound aquaporin (human) -

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Basic information

Entry
Database: PDB / ID: 9zcz
TitleC4 local refinement of stomatin-bound aquaporin (human)
ComponentsAquaporin-1
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / aquaporin / SPFH
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 / renal water transport / cerebrospinal fluid secretion / cellular response to salt stress / carbon dioxide transmembrane transport ...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 / renal water transport / cerebrospinal fluid secretion / cellular response to salt stress / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / glycerol transmembrane transporter activity / cellular response to mercury ion / water transmembrane transporter activity / 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 / intracellular water homeostasis / intracellularly cGMP-activated cation channel activity / potassium ion transmembrane transporter activity / transepithelial water transport / water channel activity / ankyrin-1 complex / ammonium transmembrane transport / ammonium channel activity / multicellular organismal-level water homeostasis / water transport / hyperosmotic response / cellular homeostasis / cellular hyperosmotic response / cell volume homeostasis / odontogenesis / nitric oxide transport / cellular response to dexamethasone stimulus / brush border / potassium ion transport / potassium channel activity / renal water homeostasis / cellular response to retinoic acid / ephrin receptor binding / transmembrane transporter activity / cellular response to nitric oxide / cellular response to cAMP / basal plasma membrane / cellular response to copper ion / Developmental Lineage of Pancreatic Ductal Cells / carbon dioxide transport / brush border membrane / positive regulation of fibroblast proliferation / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / cellular response to mechanical stimulus / sarcolemma / cellular response to hydrogen peroxide / positive regulation of angiogenesis / apical part of cell / cellular response to UV / Vasopressin regulates renal water homeostasis via Aquaporins / nuclear membrane / cellular response to hypoxia / defense response to Gram-negative bacterium / basolateral plasma membrane / apical plasma membrane / axon / negative regulation of apoptotic process / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Aquaporin 1 / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
CHOLESTEROL / PALMITIC ACID / Aquaporin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 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
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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,55712
Polymers103,9844
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 / Source: (natural) Homo sapiens (human) / References: UniProt: P29972
#2: 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
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H32O2 / 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: Local C4 refinement of aquaporin 1 within the stomatin oligomer (16mer with approximate 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
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 631000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037620
ELECTRON MICROSCOPYf_angle_d0.56710392
ELECTRON MICROSCOPYf_dihedral_angle_d7.6811148
ELECTRON MICROSCOPYf_chiral_restr0.0371268
ELECTRON MICROSCOPYf_plane_restr0.0031272

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