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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


regulation of cardiolipin metabolic process / mitochondrial prohibitin complex / : / complement component C3a binding / proteinase activated receptor binding / host-mediated perturbation of viral RNA genome replication / Processing of SMDT1 / sphingolipid binding / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / Cellular response to mitochondrial stress ...regulation of cardiolipin metabolic process / mitochondrial prohibitin complex / : / complement component C3a binding / proteinase activated receptor binding / host-mediated perturbation of viral RNA genome replication / Processing of SMDT1 / sphingolipid binding / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / Cellular response to mitochondrial stress / RIG-I signaling pathway / positive regulation of complement activation / T-helper 17 type immune response / complement component C3b binding / negative regulation of androgen receptor signaling pathway / : / positive regulation of G protein-coupled receptor signaling pathway / cellular response to interleukin-6 / positive regulation of interleukin-17 production / sister chromatid cohesion / DNA biosynthetic process / positive regulation of immunoglobulin production / progesterone receptor signaling pathway / B cell activation / mitophagy / positive regulation of smooth muscle cell proliferation / protein import into nucleus / nuclear estrogen receptor binding / antiviral innate immune response / cell periphery / mitochondrion organization / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / epigenetic regulation of gene expression / RAF activation / negative regulation of cell growth / positive regulation of non-canonical NF-kappaB signal transduction / osteoblast differentiation / histone deacetylase binding / nuclear matrix / positive regulation of neuron apoptotic process / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / transcription corepressor activity / cell migration / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / regulation of apoptotic process / positive regulation of ERK1 and ERK2 cascade / mitochondrial outer membrane / protein stabilization / mitochondrial inner membrane / negative regulation of cell population proliferation / protein heterodimerization activity / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / symbiont entry into host cell / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / cell surface / signal transduction / protein homodimerization activity / protein-containing complex / mitochondrion / DNA-templated transcription / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / 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 (eV)
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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