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- EMDB-74049: C1 local refinement of aquaporin 1 bound to endogenous human stomatin -

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Basic information

Entry
Database: EMDB / ID: EMD-74049
TitleC1 local refinement of aquaporin 1 bound to endogenous human stomatin
Map dataUnsharpened map
Sample
  • Complex: The stomatin region in contact with two AQP-1 monomers
    • Protein or peptide: Aquaporin-1
    • Protein or peptide: Stomatin
  • Ligand: PALMITIC ACID
  • Ligand: CHOLESTEROL
KeywordsOligomer / C8 symmetry / scaffold / MEMBRANE 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 / cerebrospinal fluid secretion / lipid digestion / renal water transport / corticotropin secretion ...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 / cerebrospinal fluid secretion / lipid digestion / renal water transport / corticotropin secretion / cellular response to salt stress / positive regulation of viral process / carbon dioxide transmembrane transport / secretory granule organization / 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 / lateral ventricle development / establishment or maintenance of actin cytoskeleton polarity / glycerol transmembrane transport / intracellular water homeostasis / intracellularly cGMP-activated cation channel activity / renal water absorption / potassium ion transmembrane transporter activity / transepithelial water transport / water channel activity / ankyrin-1 complex / host-mediated activation of viral genome replication / ammonium transmembrane transport / ammonium channel activity / fibroblast migration / glomerular filtration / camera-type eye morphogenesis / multicellular organismal-level water homeostasis / water transport / hyperosmotic response / regulation of monoatomic ion transmembrane transport / cellular homeostasis / cellular hyperosmotic response / odontogenesis / RNA polymerase binding / cell volume homeostasis / positive regulation of fibroblast migration / 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 / cellular response to dexamethasone stimulus / RHOA GTPase cycle / positive regulation of protein targeting to membrane / potassium channel activity / establishment of localization in cell / specific granule membrane / renal water homeostasis / ephrin receptor binding / transmembrane transporter activity / cellular response to retinoic acid / cellular response to nitric oxide / sensory perception of pain / basal plasma membrane / cellular response to cAMP / cellular response to copper ion / potassium ion transport / Developmental Lineage of Pancreatic Ductal Cells / carbon dioxide 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 / Stimuli-sensing channels / positive regulation of angiogenesis / apical part of cell / cellular response to UV / melanosome / Vasopressin regulates renal water homeostasis via Aquaporins / nuclear membrane / blood microparticle / cellular response to hypoxia / defense response to Gram-negative bacterium / vesicle / 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
Stomatin / Aquaporin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_74049.png

Downloads & links

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Map

FileDownload / File: emd_74049.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: 0.015
Minimum - Maximum-0.058247946 - 0.13322124
Average (Standard dev.)0.0017454553 (±0.0049954415)
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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Additional map: Sharpened map (B=-74.5)

Fileemd_74049_additional_1.map
AnnotationSharpened map (B=-74.5)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_74049_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_74049_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The stomatin region in contact with two AQP-1 monomers

EntireName: The stomatin region in contact with two AQP-1 monomers
Components
  • Complex: The stomatin region in contact with two AQP-1 monomers
    • Protein or peptide: Aquaporin-1
    • Protein or peptide: Stomatin
  • Ligand: PALMITIC ACID
  • Ligand: CHOLESTEROL

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Supramolecule #1: The stomatin region in contact with two AQP-1 monomers

SupramoleculeName: The stomatin region in contact with two AQP-1 monomers
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aquaporin-1

MacromoleculeName: Aquaporin-1 / type: protein_or_peptide / ID: 1 / Details: Aquaporin-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: Stomatin

MacromoleculeName: Stomatin / type: protein_or_peptide / ID: 2
Details: Stomatin region in contact with AQP-1,Stomatin region in contact with AQP-1
Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.12873 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)K GLGPCGWILV AFSFLFTVIT FPISIWMCIK IIKEYERAII FRLGRILQGG AKGPGLFFIL PCTDSFIKV DMRTISFDIP ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)K GLGPCGWILV AFSFLFTVIT FPISIWMCIK IIKEYERAII FRLGRILQGG AKGPGLFFIL PCTDSFIKV DMRTISFDIP PQEILTKDSV TISVDGVVYY RVQNATLAVA NITNADSATR LLAQTTLRNV LGTKNLSQIL SDREEIAHNM QSTLDDATD AWGIKVERVE IKDVKLP

UniProtKB: Stomatin

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Macromolecule #3: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 3 / Details: Aquaporin-1 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #4: CHOLESTEROL

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

ChemComp-CLR:
CHOLESTEROL

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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: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 135000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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