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- EMDB-70179: Structure of the human prohibitin complex in the closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-70179
TitleStructure of the human prohibitin complex in the closed state
Map data
Sample
  • Cell: Human prohibitin complex consisting of PHB1 and PHB2
    • Protein or peptide: Prohibitin-2
    • Protein or peptide: Prohibitin 1
KeywordsMitochondria / Membrane / MEMBRANE PROTEIN
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 / T-helper 17 type immune response / Cellular response to mitochondrial stress / 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 / mammary gland epithelial cell proliferation / sister chromatid cohesion / 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 / : / : / mitophagy / estrogen receptor signaling pathway / positive regulation of smooth muscle cell proliferation / antiviral innate immune response / 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 / early endosome / mitochondrial outer membrane / 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 / regulation of DNA-templated transcription / symbiont entry into host cell / negative regulation of apoptotic process / 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)
Methodsubtomogram averaging / cryo EM / Resolution: 21.0 Å
AuthorsRose K / Herrmann E / Hurley JH
Funding support United States, Germany, 4 items
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, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70179.png

Downloads & links

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Map

FileDownload / File: emd_70179.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
4.2 Å/pix.
x 120 pix.
= 504. Å		4.2 Å/pix.
x 120 pix.
= 504. Å		4.2 Å/pix.
x 120 pix.
= 504. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0002
Minimum - Maximum-0.0006150886 - 0.0024347354
Average (Standard dev.)0.000025362704 (±0.00015668389)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 503.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70179_msk_1.map
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Half map: #2

Fileemd_70179_half_map_1.map
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Half map: #1

Fileemd_70179_half_map_2.map
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Sample components

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Entire : Human prohibitin complex consisting of PHB1 and PHB2

EntireName: Human prohibitin complex consisting of PHB1 and PHB2
Components
  • Cell: Human prohibitin complex consisting of PHB1 and PHB2
    • Protein or peptide: Prohibitin-2
    • Protein or peptide: Prohibitin 1

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Supramolecule #1: Human prohibitin complex consisting of PHB1 and PHB2

SupramoleculeName: Human prohibitin complex consisting of PHB1 and PHB2 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Prohibitin-2

MacromoleculeName: Prohibitin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.341355 KDa
SequenceString: MAQNLKDLAG RLPAGPRGMG TALKLLLGAG AVAYGVRESV FTVEGGHRAI FFNRIGGVQQ DTILAEGLHF RIPWFQYPII YDIRARPRK ISSPTGSKDL QMVNISLRVL SRPNAQELPS MYQRLGLDYE ERVLPSIVNE VLKSVVAKFN ASQLITQRAQ V SLLIRREL ...String:
MAQNLKDLAG RLPAGPRGMG TALKLLLGAG AVAYGVRESV FTVEGGHRAI FFNRIGGVQQ DTILAEGLHF RIPWFQYPII YDIRARPRK ISSPTGSKDL QMVNISLRVL SRPNAQELPS MYQRLGLDYE ERVLPSIVNE VLKSVVAKFN ASQLITQRAQ V SLLIRREL TERAKDFSLI LDDVAITELS FSREYTAAVE AKQVAQQEAQ RAQFLVEKAK QEQRQKIVQA EGEAEAAKML GE ALSKNPG YIKLRKIRAA QNISKTIATS QNRIYLTADN LVLNLQDESF TRGSDSLIKG KK

UniProtKB: Prohibitin-2

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Macromolecule #2: Prohibitin 1

MacromoleculeName: Prohibitin 1 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.838029 KDa
SequenceString: MAAKVFESIG KFGLALAVAG GVVNSALYNV DAGHRAVIFD RFRGVQDIVV GEGTHFLIPW VQKPIIFDCR SRPRNVPVIT GSKDLQNVN ITLRILFRPV ASQLPRIFTS IGEDYDERVL PSITTEILKS VVARFDAGEL ITQRELVSRQ VSDDLTERAA T FGLILDDV ...String:
MAAKVFESIG KFGLALAVAG GVVNSALYNV DAGHRAVIFD RFRGVQDIVV GEGTHFLIPW VQKPIIFDCR SRPRNVPVIT GSKDLQNVN ITLRILFRPV ASQLPRIFTS IGEDYDERVL PSITTEILKS VVARFDAGEL ITQRELVSRQ VSDDLTERAA T FGLILDDV SLTHLTFGKE FTEAVEAKQV AQQEAERARF VVEKAEQQKK AAIISAEGDS KAAELIANSL ATAGDGLIEL RK LEAAEDI AYQLSRSRNI TYLPAGQSVL LQLPQ

UniProtKB: Prohibitin 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 310.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy #1

Microscopy ID1
MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 25 eV
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 43000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingImage recording ID: 2 / Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~~

Microscopy ID1
MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingImage recording ID: 3 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number subtomograms used: 1156
ExtractionNumber tomograms: 77 / Number images used: 2677 / Method: Manual picking / Software - Name: RELION (ver. 5.0)
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 3 / Avg.num./class: 800 / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9o6s:
Structure of the human prohibitin complex in the closed state

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