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- EMDB-70180: Structure of the human prohibitin complex in the open state -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-70180
TitleStructure of the human prohibitin complex in the open 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 / modulation by host of viral RNA genome replication / proteinase activated receptor binding / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of mammary gland epithelial cell proliferation / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway ...complement component C3a binding / mitochondrial prohibitin complex / regulation of cardiolipin metabolic process / regulation of cytochrome-c oxidase activity / amide binding / modulation by host of viral RNA genome replication / proteinase activated receptor binding / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of mammary gland epithelial cell proliferation / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / sphingolipid binding / Processing of SMDT1 / Cellular response to mitochondrial stress / T-helper 17 type immune response / positive regulation of exit from mitosis / RIG-I signaling pathway / negative regulation of intracellular estrogen receptor signaling pathway / positive regulation of complement activation / complement component C3b binding / mammary gland branching involved in thelarche / negative regulation of androgen receptor signaling pathway / positive regulation of cell cycle G1/S phase transition / 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 / positive regulation of immunoglobulin production / DNA biosynthetic process / positive regulation of interleukin-17 production / B cell activation / presynaptic active zone / mammary gland alveolus development / progesterone receptor signaling pathway / mitophagy / cellular response to retinoic acid / estrogen receptor signaling pathway / antiviral innate immune response / positive regulation of DNA-binding transcription factor activity / epigenetic regulation of gene expression / cell periphery / GABA-ergic synapse / nuclear estrogen receptor binding / mitochondrion organization / negative regulation of DNA-binding transcription factor activity / positive regulation of smooth muscle cell proliferation / RAF activation / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of cell growth / negative regulation of ERK1 and ERK2 cascade / negative regulation of protein catabolic process / 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 / transcription corepressor activity / osteoblast differentiation / positive regulation of neuron apoptotic process / cell migration / regulation of apoptotic process / cellular response to hypoxia / mitochondrial outer membrane / early endosome / mitochondrial inner membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / postsynaptic density / protein stabilization / protein heterodimerization activity / symbiont entry into host cell / axon / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / cell surface / 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: 22.0 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: To Be Published
Title: In situ cryo-ET visualization of mitochondrial depolarization and mitophagic engulfment
Authors: Rose KM / Herrmann E / Kakudji E / Lizarrondo J / Celebi AY / Wilfling F / Lewis SC / Hurley JH
History
DepositionApr 14, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70180.png

Downloads & links

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Map

FileDownload / File: emd_70180.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0001
Minimum - Maximum-0.0006701039 - 0.0016136656
Average (Standard dev.)0.000017068813 (±0.00012145616)
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_70180_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70180_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_70180_half_map_2.map
Projections & Slices
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Histogram (log scale)

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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
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: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1193
ExtractionNumber tomograms: 77 / Number images used: 2677 / Method: Manual picking
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 3 / Avg.num./class: 800
Final angle assignmentType: MAXIMUM LIKELIHOOD
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-9o6t:
Structure of the human prohibitin complex in the open state

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