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- PDB-9o6t: Structure of the human prohibitin complex in the open state -

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Open data


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Basic information

Entry
Database: PDB / ID: 9o6t
TitleStructure of the human prohibitin complex in the open state
Components
  • Prohibitin 1
  • Prohibitin-2
KeywordsMEMBRANE PROTEIN / Mitochondria / Membrane
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)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 22 Å
AuthorsRose, K. / Herrmann, E. / Hurley, J.H.
Funding support United States, Germany, 4items
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, K.M. / Herrmann, E. / Kakudji, E. / Lizarrondo, J. / Celebi, A.Y. / Wilfling, F. / Lewis, S.C. / Hurley, J.H.
History
DepositionApr 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prohibitin-2
B: Prohibitin 1
C: Prohibitin-2
D: Prohibitin 1
E: Prohibitin-2
F: Prohibitin 1
G: Prohibitin-2
H: Prohibitin 1
I: Prohibitin-2
J: Prohibitin 1
K: Prohibitin-2
L: Prohibitin 1
M: Prohibitin-2
N: Prohibitin 1
O: Prohibitin-2
P: Prohibitin 1
Q: Prohibitin-2
R: Prohibitin 1
S: Prohibitin-2
T: Prohibitin 1
U: Prohibitin-2
V: Prohibitin 1
W: Prohibitin-2
X: Prohibitin 1


Theoretical massNumber of molelcules
Total (without water)758,15324
Polymers758,15324
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Prohibitin-2 / B-cell receptor-associated protein BAP37 / D-prohibitin / Repressor of estrogen receptor activity


Mass: 33341.355 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: U2OS / References: UniProt: Q99623
#2: Protein
Prohibitin 1


Mass: 29838.029 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: U2OS / References: UniProt: P35232
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 consisting of PHB1 and PHB2 / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: 90 % / Chamber temperature: 310.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Alignment procedure: COMA FREE / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: TFS KRIOS / Mode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 2000 nm / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen-ID: 1

IDNominal magnification (X)
143000
264000
342000
Image recording
IDImaging-IDElectron dose (e/Å2)Avg electron dose per subtomogram (e/Å2)Film or detector model
112.190GATAN K3 BIOQUANTUM (6k x 4k)
223120FEI FALCON IV (4k x 4k)
333120GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging optics
Energyfilter nameIDImaging-IDEnergyfilter slit width (eV)
GIF Bioquantum1125
TFS Selectris X2210
GIF Bioquantum3320

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1193 / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: Manual picking / Num. of tomograms: 77 / Num. of volumes extracted: 2677
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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