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- PDB-9unl: Cryo-EM structure of the human prohibitin complex -

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Basic information

Entry
Database: PDB / ID: 9unl
TitleCryo-EM structure of the human prohibitin complex
Components
  • Prohibitin 1
  • Prohibitin-2
KeywordsMEMBRANE PROTEIN / prohibitin
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 / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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: 2.8 Å
AuthorsHong, S.X. / Guan, Z.Y. / Wang, Q. / Yin, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-EM structure of the prohibitin complex in open conformation.
Authors: Sixing Hong / Zeyuan Guan / Liying Zhang / Jinjin Zhuang / Ling Yan / Yanjun Liu / Zhu Liu / Qiang Wang / Ping Yin /
Abstract: Prohibitin 1 (PHB1) and Prohibitin 2 (PHB2), two conserved prohibitin members, are primarily localized to the mitochondrial inner membrane (MIM) to form a nanoscale macromolecular prohibitin complex. ...Prohibitin 1 (PHB1) and Prohibitin 2 (PHB2), two conserved prohibitin members, are primarily localized to the mitochondrial inner membrane (MIM) to form a nanoscale macromolecular prohibitin complex. This prohibitin complex can facilitate the spatial organization of proteins and lipids, thus maintaining cellular metabolism and homeostasis, but its architecture remains largely unknown. Here, we report the cryo-EM structure of a prohibitin complex at 2.8 Å resolution, which contains 11 PHB1-PHB2 heterodimers. This complex displays a bell-like cage, consisting of a lid and a wall, which creates an intermembrane space-facing compartment for the MIM. The lid of the cage is stably assembled, and it is responsible for the prohibitin complex formation. In contrast, the wall of the cage is flexible and exhibits lateral openings, providing a channel for intramembrane exchange of proteins and lipids. These findings provide a structural basis for understanding the scaffold role of the prohibitin complex in organizing intramembrane proteins and lipids.
History
DepositionApr 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)727,54422
Polymers727,54422
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 1


Mass: 32798.984 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 neanderthalensis (Neandertal) / 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: PHB complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding 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: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268512 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00528948
ELECTRON MICROSCOPYf_angle_d0.88839046
ELECTRON MICROSCOPYf_dihedral_angle_d11.46111040
ELECTRON MICROSCOPYf_chiral_restr0.0474551
ELECTRON MICROSCOPYf_plane_restr0.0075118

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