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- EMDB-19459: The human prohibitin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-19459
TitleThe human prohibitin complex
Map dataFinal map resulting from 3D Refinement of ~820 subtomograms (pixel size 2.5 Apx) in Relion 4.0
Sample
  • Cell: human prohibitin complex formed by PHB1 and PHB2
    • Protein or peptide: Prohibitin 1
    • Protein or peptide: Prohibitin-2
KeywordsChaperone / Lipid organization / Protease regulator / 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: 16.3 Å
AuthorsLange F / Ratz M / Dohrke JN / Wenzel D / Riedel D / Ilgen P / Jakobs S
Funding support Germany, European Union, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)2067/1- 390729940 Germany
European Research Council (ERC)ERCAdG No. 835102European Union
German Research Foundation (DFG)TRR 274 Germany
German Research Foundation (DFG)SFB 1456 Germany
German Research Foundation (DFG)FOR 2848 Germany
CitationJournal: Nat Cell Biol / Year: 2025
Title: In situ architecture of the human prohibitin complex.
Authors: Felix Lange / Michael Ratz / Jan-Niklas Dohrke / Maxence Le Vasseur / Dirk Wenzel / Peter Ilgen / Dietmar Riedel / Stefan Jakobs /
Abstract: Prohibitins are a highly conserved family of proteins that have been implicated in a variety of functions including mitochondrial stress signalling and housekeeping, cell cycle progression, ...Prohibitins are a highly conserved family of proteins that have been implicated in a variety of functions including mitochondrial stress signalling and housekeeping, cell cycle progression, apoptosis, lifespan regulation and many others. The human prohibitins prohibitin 1 and prohibitin 2 have been proposed to act as scaffolds within the mitochondrial inner membrane, but their molecular organization has remained elusive. Here we determined the molecular organization of the human prohibitin complex within the mitochondrial inner membrane using an integrative structural biology approach combining quantitative western blotting, cryo-electron tomography, subtomogram averaging and molecular modelling. The proposed bell-shaped structure consists of 11 alternating prohibitin 1 and prohibitin 2 molecules. This study reveals an average of about 43 prohibitin complexes per crista, covering 1-3% of the crista membrane area. These findings provide a structural basis for understanding the functional contributions of prohibitins to the integrity and spatial organization of the mitochondrial inner membrane.
History
DepositionJan 22, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19459.png

Downloads & links

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Map

FileDownload / File: emd_19459.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map resulting from 3D Refinement of ~820 subtomograms (pixel size 2.5 Apx) in Relion 4.0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 120 pix.
= 300. Å		2.5 Å/pix.
x 120 pix.
= 300. Å		2.5 Å/pix.
x 120 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.3215648 - 0.436925
Average (Standard dev.)0.015586674 (±0.09031375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19459_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 02 no solvent flattening

Fileemd_19459_half_map_1.map
AnnotationHalf Map 02 no solvent flattening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 01 no solvent flattening

Fileemd_19459_half_map_2.map
AnnotationHalf Map 01 no solvent flattening
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 prohibitin complex formed by PHB1 and PHB2

EntireName: human prohibitin complex formed by PHB1 and PHB2
Components
  • Cell: human prohibitin complex formed by PHB1 and PHB2
    • Protein or peptide: Prohibitin 1
    • Protein or peptide: Prohibitin-2

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Supramolecule #1: human prohibitin complex formed by PHB1 and PHB2

SupramoleculeName: human prohibitin complex formed by PHB1 and PHB2 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Details: 11 molecules of PHB1 and PHB2 form the human prohibitin complex
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Prohibitin 1

MacromoleculeName: Prohibitin 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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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Macromolecule #2: Prohibitin-2

MacromoleculeName: Prohibitin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: DMEM high glucose medium (Gibco)
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K / Max: 93.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4 / Average exposure time: 0.53 sec. / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 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

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C11 (11 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 16.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 817
ExtractionNumber tomograms: 37 / Number images used: 817 / Reference model: none / Method: manual picking
Software:
Namedetails
Dynamo (ver. 1.1.532)Particle picking and initial pose optimization
Warp (ver. 1.0.9)Subtomogram extraction
Final 3D classificationNumber classes: 1 / Avg.num./class: 817 / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
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: FLEXIBLE FIT
Output model

PDB-8rrh:
The human prohibitin complex

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