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- PDB-9o9z: The human PHB1/2 complex (closed) -

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Basic information

Entry
Database: PDB / ID: 9o9z
TitleThe human PHB1/2 complex (closed)
Components
  • Prohibitin 1
  • Prohibitin-2
KeywordsMEMBRANE PROTEIN / SPFH / Mitochondria / PHB1 / PHB2
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 / T-helper 17 type immune response ...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 / T-helper 17 type immune response / Cellular response to mitochondrial stress / RIG-I signaling pathway / positive regulation of complement activation / 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 / sister chromatid cohesion / DNA biosynthetic process / positive regulation of immunoglobulin production / positive regulation of interleukin-17 production / progesterone receptor signaling pathway / B cell activation / mitophagy / positive regulation of smooth muscle cell proliferation / epigenetic regulation of gene expression / nuclear estrogen receptor binding / antiviral innate immune response / cell periphery / mitochondrion organization / negative regulation of protein catabolic process / protein import into nucleus / negative regulation of ERK1 and ERK2 cascade / RAF activation / negative regulation of cell growth / positive regulation of non-canonical NF-kappaB signal transduction / histone deacetylase binding / osteoblast differentiation / nuclear matrix / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / transcription corepressor activity / positive regulation of neuron apoptotic process / cell migration / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / positive regulation of ERK1 and ERK2 cascade / mitochondrial outer membrane / mitochondrial inner membrane / protein stabilization / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / symbiont entry into host cell / regulation of DNA-templated transcription / negative regulation of apoptotic process / 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 / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsGao, J. / Shao, S. / Sherpa, D. / Kupko, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG073277 United States
David and Lucile Packard Foundation United States
Richard and Susan Smith Family Foundation United States
CitationJournal: Nat Commun / Year: 2025
Title: Structures of human organellar SPFH protein complexes.
Authors: Jingjing Gao / Dawafuti Sherpa / Nikita Kupko / Haruka Chino / Jianwei Zeng / Sichen Shao /
Abstract: Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are found in all kingdoms of life and in multiple eukaryotic organelles. SPFH proteins assemble into homo- or hetero-oligomeric ...Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are found in all kingdoms of life and in multiple eukaryotic organelles. SPFH proteins assemble into homo- or hetero-oligomeric rings that form domed structures. Most SPFH assemblies also abut a cellular membrane, where they are implicated in diverse functions ranging from membrane organization to protein quality control. However, the precise architectures of different SPFH complexes remain unclear. Here, we report single-particle cryo-EM structures of the endoplasmic reticulum (ER)-resident Erlin1/2 complex and the mitochondrial prohibitin (PHB1/2) complex, revealing assemblies of 13 heterodimers of Erlin1 and Erlin2 and 11 heterodimers of PHB1 and PHB2, respectively. We also describe key interactions underlying the architecture of each complex and conformational heterogeneity of the PHB1/2 complex. Our findings elucidate the distinct stoichiometries and properties of human organellar SPFH complexes and highlight common principles of SPFH complex organization.
History
DepositionApr 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
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Revision 1.1Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prohibitin 1
B: Prohibitin 1
C: Prohibitin 1
D: Prohibitin 1
E: Prohibitin 1
F: Prohibitin 1
G: Prohibitin 1
H: Prohibitin 1
I: Prohibitin 1
J: Prohibitin 1
K: Prohibitin 1
a: Prohibitin-2
b: Prohibitin-2
c: Prohibitin-2
d: Prohibitin-2
e: Prohibitin-2
f: Prohibitin-2
g: Prohibitin-2
h: Prohibitin-2
i: Prohibitin-2
j: Prohibitin-2
k: Prohibitin-2


Theoretical massNumber of molelcules
Total (without water)732,93022
Polymers732,93022
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: 33288.652 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHB1, PHB / Production host: Homo sapiens (human) / 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.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHB2, BAP, REA / Production host: 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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human PHB1/2 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C11 (11 fold cyclic)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22299 / Symmetry type: POINT

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