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- PDB-9o6t: Structure of the human prohibitin complex in the open state -

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Open data


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Basic information

Entry
Database: PDB / ID: 9o6t
TitleStructure of the human prohibitin complex in the open state
Components
  • Prohibitin 1
  • Prohibitin-2
KeywordsMEMBRANE PROTEIN / Mitochondria / Membrane
Function / homology
Function and homology information


complement component C3a binding / mitochondrial prohibitin complex / regulation of cardiolipin metabolic process / regulation of cytochrome-c oxidase activity / amide binding / host-mediated perturbation of viral RNA genome replication / proteinase activated receptor binding / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of mammary gland epithelial cell proliferation ...complement component C3a binding / mitochondrial prohibitin complex / regulation of cardiolipin metabolic process / regulation of cytochrome-c oxidase activity / amide binding / host-mediated perturbation of viral RNA genome replication / proteinase activated receptor binding / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of mammary gland epithelial cell proliferation / sphingolipid binding / Processing of SMDT1 / Cellular response to mitochondrial stress / T-helper 17 type immune response / RIG-I signaling pathway / positive regulation of complement activation / complement component C3b binding / mammary gland branching involved in thelarche / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of androgen receptor signaling pathway / negative regulation of transcription by competitive promoter binding / positive regulation of G protein-coupled receptor signaling pathway / cellular response to interleukin-6 / sister chromatid cohesion / mammary gland epithelial cell proliferation / DNA biosynthetic process / positive regulation of immunoglobulin production / positive regulation of interleukin-17 production / B cell activation / progesterone receptor signaling pathway / mammary gland alveolus development / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / mitophagy / estrogen receptor signaling pathway / antiviral innate immune response / positive regulation of smooth muscle cell proliferation / epigenetic regulation of gene expression / nuclear estrogen receptor binding / cell periphery / mitochondrion organization / RAF activation / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of cell growth / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / histone deacetylase binding / nuclear matrix / protein import into nucleus / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / osteoblast differentiation / transcription corepressor activity / cell migration / positive regulation of neuron apoptotic process / regulation of apoptotic process / mitochondrial outer membrane / early endosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitochondrial inner membrane / protein stabilization / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / symbiont entry into host cell / negative regulation of apoptotic process / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Prohibitin / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Prohibitin 1 / Prohibitin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 22 Å
AuthorsRose, K. / Herrmann, E. / Hurley, J.H.
Funding support United States, Germany, 4items
OrganizationGrant numberCountry
Aligning Science Across Parkinsons (ASAP)ASAP-000350 United States
Alexander von Humboldt Foundation Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM139168 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM139166 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: In situ cryo-ET visualization of mitochondrial depolarization and mitophagic engulfment.
Authors: Kevin Rose / Eric Herrmann / Eve Kakudji / Javier Lizarrondo / A Yasemin Celebi / Florian Wilfling / Samantha C Lewis / James H Hurley /
Abstract: Defective mitochondrial quality control in response to loss of mitochondrial membrane polarization is implicated in Parkinson's disease by mutations in and . Parkin-expressing U2 osteosarcoma (U2OS) ...Defective mitochondrial quality control in response to loss of mitochondrial membrane polarization is implicated in Parkinson's disease by mutations in and . Parkin-expressing U2 osteosarcoma (U2OS) cells were treated with the depolarizing agents oligomycin and antimycin A (OA) and subjected to cryo-focused ion beam milling and in situ cryo-electron tomography. Mitochondria were fragmented and devoid of matrix calcium phosphate crystals. Phagophores were visualized, with bridge-like lipid transporter densities connected to mitophagic phagophores. A subpopulation of ATP synthases relocalized from cristae to the inner boundary membrane. The structure of the dome-shaped prohibitin complex, a dodecamer of PHB1-PHB2 dimers, was determined in situ by subtomogram averaging in untreated and treated cells and found to exist in open and closed conformations, with the closed conformation being enriched by OA treatment. These findings provide a set of native snapshots of the manifold nano-structural consequences of mitochondrial depolarization and provide a baseline for future in situ dissection of Parkin-dependent mitophagy.
History
DepositionApr 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0May 7, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prohibitin-2
B: Prohibitin 1
C: Prohibitin-2
D: Prohibitin 1
E: Prohibitin-2
F: Prohibitin 1
G: Prohibitin-2
H: Prohibitin 1
I: Prohibitin-2
J: Prohibitin 1
K: Prohibitin-2
L: Prohibitin 1
M: Prohibitin-2
N: Prohibitin 1
O: Prohibitin-2
P: Prohibitin 1
Q: Prohibitin-2
R: Prohibitin 1
S: Prohibitin-2
T: Prohibitin 1
U: Prohibitin-2
V: Prohibitin 1
W: Prohibitin-2
X: Prohibitin 1


Theoretical massNumber of molelcules
Total (without water)758,15324
Polymers758,15324
Non-polymers00
Water00
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
Prohibitin-2 / B-cell receptor-associated protein BAP37 / D-prohibitin / Repressor of estrogen receptor activity


Mass: 33341.355 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: U2OS / References: UniProt: Q99623
#2: Protein
Prohibitin 1


Mass: 29838.029 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: U2OS / References: UniProt: P35232
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Human prohibitin complex consisting of PHB1 and PHB2 / Type: CELL / Entity ID: all / Source: NATURAL
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 / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 310.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Alignment procedure: COMA FREE / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: TFS KRIOS / Mode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 2000 nm / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen-ID: 1

IDNominal magnification (X)
143000
264000
342000
Image recording
IDImaging-IDElectron dose (e/Å2)Avg electron dose per subtomogram (e/Å2)Film or detector model
112.190GATAN K3 BIOQUANTUM (6k x 4k)
223120FEI FALCON IV (4k x 4k)
333120GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging optics
Energyfilter nameIDImaging-IDEnergyfilter slit width (eV)
GIF Bioquantum1125
TFS Selectris X2210
GIF Bioquantum3320

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1193 / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: Manual picking / Num. of tomograms: 77 / Num. of volumes extracted: 2677
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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