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- PDB-9z7u: Human Stomatin - C8 Symmetry -

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Basic information

Entry
Database: PDB / ID: 9z7u
TitleHuman Stomatin - C8 Symmetry
ComponentsStomatin
KeywordsMEMBRANE PROTEIN / Oligomer / C8 symmetry / scaffold
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsVallese, F. / Clarke, O.B.
Funding support1items
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, O.B.
History
DepositionNov 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Stomatin
G: Stomatin
B: Stomatin
C: Stomatin
E: Stomatin
H: Stomatin
J: Stomatin
K: Stomatin
M: Stomatin
N: Stomatin
P: Stomatin
Q: Stomatin
S: Stomatin
T: Stomatin
V: Stomatin
W: Stomatin


Theoretical massNumber of molelcules
Total (without water)475,70816
Polymers475,70816
Non-polymers00
Water17,727984
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Stomatin / Erythrocyte band 7 integral membrane protein / Erythrocyte membrane protein band 7.2 / Protein 7.2b


Mass: 29731.721 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27105
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 984 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Stomatin oligomer formed by 16 subunits with C8 symmetry.
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00433328
ELECTRON MICROSCOPYf_angle_d0.60845240
ELECTRON MICROSCOPYf_dihedral_angle_d5.6474648
ELECTRON MICROSCOPYf_chiral_restr0.0455552
ELECTRON MICROSCOPYf_plane_restr0.0055736

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