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- EMDB-64355: Cryo-EM structure of the human prohibitin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64355
TitleCryo-EM structure of the human prohibitin complex
Map data
Sample
  • Complex: PHB complex
    • Protein or peptide: Prohibitin 1
    • Protein or peptide: Prohibitin-2
Keywordsprohibitin / MEMBRANE PROTEIN
Function / homology
Function and homology information


mitochondrial prohibitin complex / regulation of cardiolipin metabolic process / regulation of cytochrome-c oxidase activity / : / complement component C3a binding / proteinase activated receptor binding / host-mediated perturbation of viral RNA genome replication / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of mammary gland epithelial cell proliferation / Processing of SMDT1 ...mitochondrial prohibitin complex / regulation of cardiolipin metabolic process / regulation of cytochrome-c oxidase activity / : / complement component C3a binding / proteinase activated receptor binding / host-mediated perturbation of viral RNA genome replication / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of mammary gland epithelial cell proliferation / 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 / mammary gland branching involved in thelarche / complement component C3b binding / negative regulation of intracellular estrogen receptor signaling pathway / : / negative regulation of androgen receptor signaling pathway / positive regulation of G protein-coupled receptor signaling pathway / cellular response to interleukin-6 / mammary gland epithelial cell proliferation / sister chromatid cohesion / positive regulation of immunoglobulin production / DNA biosynthetic process / positive regulation of interleukin-17 production / progesterone receptor signaling pathway / B cell activation / mammary gland alveolus development / : / : / mitophagy / estrogen receptor signaling pathway / epigenetic regulation of gene expression / positive regulation of smooth muscle cell proliferation / antiviral innate immune response / nuclear estrogen receptor binding / cell periphery / mitochondrion organization / RAF activation / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of cell growth / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / nuclear matrix / histone deacetylase binding / 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 / osteoblast differentiation / transcription corepressor activity / positive regulation of neuron apoptotic process / cell migration / regulation of apoptotic process / early endosome / mitochondrial outer membrane / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / symbiont entry into host cell / regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / protein-containing complex / mitochondrion / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHong SX / Guan ZY / Wang Q / Yin P
Funding support China, 1 items
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, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64355.png

Downloads & links

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Map

FileDownload / File: emd_64355.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.0022920726 - 1.6939622
Average (Standard dev.)0.00064681633 (±0.016675727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64355_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

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Half map: #1

Fileemd_64355_half_map_2.map
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Histogram (log scale)

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Sample components

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Entire : PHB complex

EntireName: PHB complex
Components
  • Complex: PHB complex
    • Protein or peptide: Prohibitin 1
    • Protein or peptide: Prohibitin-2

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Supramolecule #1: PHB complex

SupramoleculeName: PHB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Prohibitin 1

MacromoleculeName: Prohibitin 1 / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.798984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAKVFESIG KFGLALAVAG GVVNSALYNV DAGHRAVIFD RFRGVQDIVV GEGTHFLIPW VQKPIIFDCR SRPRNVPVIT GSKDLQNVN ITLRILFRPV ASQLPRIFTS IGEDYDERVL PSITTEILKS VVARFDAGEL ITQRELVSRQ VSDDLTERAA T FGLILDDV ...String:
MAAKVFESIG KFGLALAVAG GVVNSALYNV DAGHRAVIFD RFRGVQDIVV GEGTHFLIPW VQKPIIFDCR SRPRNVPVIT GSKDLQNVN ITLRILFRPV ASQLPRIFTS IGEDYDERVL PSITTEILKS VVARFDAGEL ITQRELVSRQ VSDDLTERAA T FGLILDDV SLTHLTFGKE FTEAVEAKQV AQQEAERARF VVEKAEQQKK AAIISAEGDS KAAELIANSL ATAGDGLIEL RK LEAAEDI AYQLSRSRNI TYLPAGQSVL LQLPQLEDYK DHDGDYKDHD IDYKDDDDK

UniProtKB: Prohibitin 1

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Macromolecule #2: Prohibitin-2

MacromoleculeName: Prohibitin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.341355 KDa
Recombinant expressionOrganism: Homo sapiens neanderthalensis (Neandertal)
SequenceString: MAQNLKDLAG RLPAGPRGMG TALKLLLGAG AVAYGVRESV FTVEGGHRAI FFNRIGGVQQ DTILAEGLHF RIPWFQYPII YDIRARPRK ISSPTGSKDL QMVNISLRVL SRPNAQELPS MYQRLGLDYE ERVLPSIVNE VLKSVVAKFN ASQLITQRAQ V SLLIRREL ...String:
MAQNLKDLAG RLPAGPRGMG TALKLLLGAG AVAYGVRESV FTVEGGHRAI FFNRIGGVQQ DTILAEGLHF RIPWFQYPII YDIRARPRK ISSPTGSKDL QMVNISLRVL SRPNAQELPS MYQRLGLDYE ERVLPSIVNE VLKSVVAKFN ASQLITQRAQ V SLLIRREL TERAKDFSLI LDDVAITELS FSREYTAAVE AKQVAQQEAQ RAQFLVEKAK QEQRQKIVQA EGEAEAAKML GE ALSKNPG YIKLRKIRAA QNISKTIATS QNRIYLTADN LVLNLQDESF TRGSDSLIKG KK

UniProtKB: Prohibitin-2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 268512
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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