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- EMDB-73881: Human Stomatin - C8 Symmetry -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-73881
TitleHuman Stomatin - C8 Symmetry
Map dataUnsharpened map
Sample
  • Complex: Stomatin oligomer formed by 16 subunits with C8 symmetry.
    • Protein or peptide: Stomatin
  • Ligand: water
KeywordsOligomer / C8 symmetry / scaffold / MEMBRANE PROTEIN
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: 2.0 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 17, 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_73881.png

Downloads & links

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Map

FileDownload / File: emd_73881.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: 0.0321
Minimum - Maximum-0.057359215 - 0.18816353
Average (Standard dev.)0.00009367331 (±0.005483702)
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_73881_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_73881_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_73881_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_73881_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 : 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: water

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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: 16 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.731721 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 IKDVKLPVQL QRAMAAEAEA SREARAKVIA AEGEMNASRA LKEASMVITE SPAALQLRYL Q TLTTIAAE KNSTIVFPLP IDMLQGII

UniProtKB: Stomatin

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 984 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
GridMaterial: GOLD
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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 38000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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