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- EMDB-74052: Human Stomatin - intramembrane region -

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Basic information

Entry
Database: EMDB / ID: EMD-74052
TitleHuman Stomatin - intramembrane region
Map dataUnsharpened Map
Sample
  • Complex: Stomatin oligomer formed by 16 subunits with C8 symmetry.
    • Protein or peptide: Stomatin
  • Ligand: PALMITIC ACID
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
KeywordsOligomer / C8 symmetry / scaffold / MEMBRANE PROTEIN / intramembrane region
Function / homology
Function and homology information


positive regulation of viral process / host-mediated activation of viral genome replication / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / azurophil granule membrane / RHOB GTPase cycle / RHOC GTPase cycle / RHOJ GTPase cycle / ion channel inhibitor activity / RHOQ GTPase cycle ...positive regulation of viral process / host-mediated activation of viral genome replication / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / azurophil granule membrane / RHOB GTPase cycle / RHOC GTPase cycle / RHOJ GTPase cycle / ion channel inhibitor activity / RHOQ GTPase cycle / CDC42 GTPase cycle / tertiary granule membrane / RHOH GTPase cycle / RHOA GTPase cycle / positive regulation of protein targeting to membrane / specific granule membrane / Stimuli-sensing channels / melanosome / blood microparticle / vesicle / cytoskeleton / membrane raft / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / mitochondrion / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 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) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74052.png

Downloads & links

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Map

FileDownload / File: emd_74052.map.gz / Format: CCP4 / Size: 347.6 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 450 pix.
= 374.85 Å		0.83 Å/pix.
x 450 pix.
= 374.85 Å		0.83 Å/pix.
x 450 pix.
= 374.85 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: 0.021
Minimum - Maximum-0.3066474 - 0.46556303
Average (Standard dev.)0.00038210652 (±0.004304629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 374.85 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74052_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_74052_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 B

Fileemd_74052_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_74052_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 : Stomatin oligomer formed by 16 subunits with C8 symmetry.

EntireName: Stomatin oligomer formed by 16 subunits with C8 symmetry.
Components
  • Complex: Stomatin oligomer formed by 16 subunits with C8 symmetry.
    • Protein or peptide: Stomatin
  • Ligand: PALMITIC ACID
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

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Supramolecule #1: Stomatin oligomer formed by 16 subunits with C8 symmetry.

SupramoleculeName: Stomatin oligomer formed by 16 subunits with C8 symmetry.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Stomatin

MacromoleculeName: Stomatin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / 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 #2: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 2 / Number of copies: 12 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #3: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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Macromolecule #4: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

MacromoleculeName: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
type: ligand / ID: 4 / Number of copies: 4 / Formula: S1P
Molecular weightTheoretical: 379.472 Da
Chemical component information

ChemComp-S1P:
(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

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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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2151648
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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