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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 / renal water absorption / 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 / potassium ion transmembrane transporter activity / transepithelial water transport / 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 / 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 / transmembrane transporter activity / potassium channel activity / renal water homeostasis / ephrin receptor binding / cellular response to retinoic acid / cellular response to nitric oxide / sensory perception of pain / basal plasma membrane / cellular response to copper ion / cellular response to cAMP / establishment of localization in cell / 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 / apical part of cell / positive regulation of angiogenesis / cellular response to UV / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to hypoxia / nuclear membrane / basolateral plasma membrane / defense response to Gram-negative bacterium / 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: To Be Published
Title: Stomatin encapsulates aquaporin-1 and urea transporter-B in the erythrocyte membrane
Authors: Vallese F / Li H / Clarke OB
History
DepositionNov 24, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened Map

Fileemd_74046_additional_1.map
Annotationsharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_74046_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_74046_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 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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