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- EMDB-70485: Human Stomatin Complex in Native Membrane Vesicles -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70485
TitleHuman Stomatin Complex in Native Membrane Vesicles
Map dataHuman Stomatin
Sample
  • Complex: Human stomatin
    • Protein or peptide: Stomatin
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsStomatin / SPFH domain protein / Membrane microdomain / Lipid raft / Membrane-associated protein / Homo-oligomer / Membrane curvature / 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 / ion channel inhibitor activity / RHOC GTPase cycle / RHOJ GTPase cycle / 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 / ion channel inhibitor activity / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / tertiary granule membrane / CDC42 GTPase cycle / 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 / intracellular membrane-bounded organelle / 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
AuthorsStoner J / Fu Z
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Human Stomatin Complex in Native Membrane Vesicles at 2.2 Angstroms Resolution
Authors: Stoner J / Fu Z
History
DepositionMay 3, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70485.png

Downloads & links

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Map

FileDownload / File: emd_70485.map.gz / Format: CCP4 / Size: 316.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Stomatin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 436 pix.
= 367.984 Å		0.84 Å/pix.
x 436 pix.
= 367.984 Å		0.84 Å/pix.
x 436 pix.
= 367.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.064
Minimum - Maximum-0.3639476 - 0.5880347
Average (Standard dev.)0.00060654816 (±0.015685773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions436436436
Spacing436436436
CellA=B=C: 367.98398 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map2

Fileemd_70485_half_map_1.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map1

Fileemd_70485_half_map_2.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human stomatin

EntireName: Human stomatin
Components
  • Complex: Human stomatin
    • Protein or peptide: Stomatin
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: Human stomatin

SupramoleculeName: Human stomatin / 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: 33.950137 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGGGGSPSRL EEELRRRLTE PAEKRHTRDS EAQRLPDSFK DSPSKGLGPC GWILVAFSFL FTVITFPISI WMCIKIIKEY ERAIIFRLG RILQGGAKGP GLFFILPCTD SFIKVDMRTI SFDIPPQEIL TKDSVTISVD GVVYYRVQNA TLAVANITNA D SATRLLAQ ...String:
MGGGGSPSRL EEELRRRLTE PAEKRHTRDS EAQRLPDSFK DSPSKGLGPC GWILVAFSFL FTVITFPISI WMCIKIIKEY ERAIIFRLG RILQGGAKGP GLFFILPCTD SFIKVDMRTI SFDIPPQEIL TKDSVTISVD GVVYYRVQNA TLAVANITNA D SATRLLAQ TTLRNVLGTK NLSQILSDRE EIAHNMQSTL DDATDAWGIK VERVEIKDVK LPVQLQRAMA AEAEASREAR AK VIAAEGE MNASRALKEA SMVITESPAA LQLRYLQTLT TIAAEKNSTI VFPLPIDMLQ GIIGAKHSHL G

UniProtKB: Stomatin

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 16
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 942 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 / Details: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 698428
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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