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- EMDB-74047: C3 local refinement of Urea Transporter B (SLC14A1) bound to huma... -

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Basic information

Entry
Database: EMDB / ID: EMD-74047
TitleC3 local refinement of Urea Transporter B (SLC14A1) bound to human stomatin oligomer
Map dataUnsharpened map
Sample
  • Complex: Local refinement of UT-B in complex with Stomatin.
    • Protein or peptide: Urea transporter 1
  • Ligand: PHOSPHATIDYLETHANOLAMINE
KeywordsMembrane protein / solute carrier / SLC / SPFH / TRANSPORT PROTEIN
Function / homology
Function and homology information


urea channel activity / water transmembrane transporter activity / urea transport / : / urea transmembrane transport / urea transmembrane transporter activity / establishment of localization in cell / transmembrane transport / basolateral plasma membrane / plasma membrane
Similarity search - Function
Urea transporter / Urea transporter / Ammonium/urea transporter
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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_74047.png

Downloads & links

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Map

FileDownload / File: emd_74047.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: 0.03
Minimum - Maximum-0.049696047 - 0.098318376
Average (Standard dev.)0.0015589198 (±0.0051506143)
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_74047_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map (B=-61.8)

Fileemd_74047_additional_1.map
AnnotationSharpened map (B=-61.8)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_74047_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_74047_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Local refinement of UT-B in complex with Stomatin.

EntireName: Local refinement of UT-B in complex with Stomatin.
Components
  • Complex: Local refinement of UT-B in complex with Stomatin.
    • Protein or peptide: Urea transporter 1
  • Ligand: PHOSPHATIDYLETHANOLAMINE

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Supramolecule #1: Local refinement of UT-B in complex with Stomatin.

SupramoleculeName: Local refinement of UT-B in complex with Stomatin. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Urea transporter 1

MacromoleculeName: Urea transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.753828 KDa
SequenceString: FPKALGYVTG DMKELANQLK DKPVVLQFID WILRGISQVV FVNNPVSGIL ILVGLLVQNP WWALTGWLGT VVSTLMALLL SQDRSLIAS GLYGYNATLV GVLMAVFSDK GDYFWWLLLP VCAMSMTCPI FSSALNSVLS KWDLPVFTLP FNMALSMYLS A TGHYNPFF ...String:
FPKALGYVTG DMKELANQLK DKPVVLQFID WILRGISQVV FVNNPVSGIL ILVGLLVQNP WWALTGWLGT VVSTLMALLL SQDRSLIAS GLYGYNATLV GVLMAVFSDK GDYFWWLLLP VCAMSMTCPI FSSALNSVLS KWDLPVFTLP FNMALSMYLS A TGHYNPFF PAKLVIPITT APQISWSDLS ALELLKSIPV GVGQIYGCDN PWTGGIFLGA ILLSSPLMCL HAAIGSLLGI AA GLSLSAP FENIYFGLWG FNSSLACIAM GGMFMALTWQ THLLALGCAL FTAYLGVGMA NFMAEVGLPA CTWPFCLATL LFL IMTTKN SNIYKMPLSK VTYPEENRIF YLQAKKRMV

UniProtKB: Urea transporter 1

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Macromolecule #2: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 6 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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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: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 258739
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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