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- EMDB-74046: C4 local refinement of stomatin-bound aquaporin (human) -

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Basic information

Entry
Database: EMDB / ID: EMD-74046
TitleC4 local refinement of stomatin-bound aquaporin (human)
Map dataUnsharpened Map
Sample
  • Complex: Local C4 refinement of aquaporin 1 within the stomatin oligomer (16mer with approximate C8 symmetry).
    • Protein or peptide: Aquaporin-1
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID
KeywordsMEMBRANE PROTEIN / aquaporin / SPFH / TRANSPORT PROTEIN
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 / 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 / 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 / cell volume homeostasis / hyperosmotic response / positive regulation of fibroblast migration / odontogenesis / nitric oxide transport / brush border / cellular response to dexamethasone stimulus / potassium channel activity / transmembrane transporter activity / 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 / positive regulation of fibroblast proliferation / 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsVallese F / Clarke OB
Funding support1 items
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, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74046.png

Downloads & links

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Map

FileDownload / File: emd_74046.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.9 Å		0.83 Å/pix.
x 300 pix.
= 249.9 Å		0.83 Å/pix.
x 300 pix.
= 249.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0288
Minimum - Maximum-0.05384924 - 0.12888238
Average (Standard dev.)0.0013664209 (±0.004711708)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74046_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: sharpened Map

Fileemd_74046_additional_1.map
Annotationsharpened Map
Projections & Slices
AxesZYX

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Histogram

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Half map: Half map A

Fileemd_74046_half_map_1.map
AnnotationHalf map A
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_74046_half_map_2.map
AnnotationHalf Map B
Projections & Slices
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Sample components

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Entire : Local C4 refinement of aquaporin 1 within the stomatin oligomer (...

EntireName: Local C4 refinement of aquaporin 1 within the stomatin oligomer (16mer with approximate C8 symmetry).
Components
  • Complex: Local C4 refinement of aquaporin 1 within the stomatin oligomer (16mer with approximate C8 symmetry).
    • Protein or peptide: Aquaporin-1
  • Ligand: CHOLESTEROL
  • Ligand: PALMITIC ACID

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Supramolecule #1: Local C4 refinement of aquaporin 1 within the stomatin oligomer (...

SupramoleculeName: Local C4 refinement of aquaporin 1 within the stomatin oligomer (16mer with approximate C8 symmetry).
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aquaporin-1

MacromoleculeName: Aquaporin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.996072 KDa
SequenceString: SEFKKKLFWR AVVAEFLATT LFVFISIGSA LGFKYPVGNN QTAVQDNVKV SLAFGLSIAT LAQSVGHISG AHLNPAVTLG LLLSCQISI FRALMYIIAQ CVGAIVATAI LSGITSSLTG NSLGRNDLAD GVNSGQGLGI EIIGTLQLVL CVLATTDRRR R DLGGSAPL ...String:
SEFKKKLFWR AVVAEFLATT LFVFISIGSA LGFKYPVGNN QTAVQDNVKV SLAFGLSIAT LAQSVGHISG AHLNPAVTLG LLLSCQISI FRALMYIIAQ CVGAIVATAI LSGITSSLTG NSLGRNDLAD GVNSGQGLGI EIIGTLQLVL CVLATTDRRR R DLGGSAPL AIGLSVALGH LLAIDYTGCG INPARSFGSA VITHNFSNHW IFWVGPFIGG ALAVLIYDFI LAPRSSDLTD RV KVWTSGQ

UniProtKB: Aquaporin-1

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 631000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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