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- PDB-8rrh: The human prohibitin complex -

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Basic information

Entry
Database: PDB / ID: 8rrh
TitleThe human prohibitin complex
Components
  • Prohibitin 1
  • Prohibitin-2
KeywordsMEMBRANE PROTEIN / Chaperone / Lipid organization / Protease regulator
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 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 / host-mediated perturbation 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)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 16.3 Å
AuthorsLange, F. / Ratz, M. / Dohrke, J.N. / Wenzel, D. / Riedel, D. / Ilgen, P. / Jakobs, S.
Funding support Germany, European Union, 5items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Apr 23, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prohibitin 1
B: Prohibitin-2
C: Prohibitin 1
D: Prohibitin-2
E: Prohibitin 1
F: Prohibitin-2
G: Prohibitin 1
H: Prohibitin-2
I: Prohibitin 1
J: Prohibitin-2
K: Prohibitin 1


Theoretical massNumber of molelcules
Total (without water)345,73511
Polymers345,73511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Prohibitin 1


Mass: 29838.029 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: U2OS / References: UniProt: P35232
#2: Protein
Prohibitin-2 / B-cell receptor-associated protein BAP37 / D-prohibitin / Repressor of estrogen receptor activity


Mass: 33341.355 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99623
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 formed by PHB1 and PHB2 / Type: CELL
Details: 11 molecules of PHB1 and PHB2 form the human prohibitin complex
Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Cellular location: mitochondrial inner membrane / Organelle: mitochondria
Buffer solutionpH: 7.4 / Details: DMEM high glucose medium (Gibco)
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: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93 K / Temperature (min): 80 K
Image recordingAverage exposure time: 0.53 sec. / Electron dose: 120 e/Å2 / Avg electron dose per subtomogram: 120 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 4
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails
1Dynamo1.1.532volume selectionParticle picking and initial pose optimization
2Warp1.0.9volume selectionSubtomogram extraction
3SerialEM4.1image acquisition
5RELION4CTF correction
12RELION4final Euler assignment
13RELION4classification
14RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C11 (11 fold cyclic)
3D reconstructionResolution: 16.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 817 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: manual picking / Num. of tomograms: 37 / Num. of volumes extracted: 817 / Reference model: none
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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