[English] 日本語
Yorodumi
- EMDB-64355: Cryo-EM structure of the human prohibitin complex -

+
Open data


ID or keywords:

Loading...

-
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


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)
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

-
Structure visualization

Supplemental images

emd_64355.png

Downloads & links

-
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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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 °

-
Supplemental data

-
Half map: #2

Fileemd_64355_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64355_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PHB complex

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

-
Supramolecule #1: PHB complex

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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more