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- EMDB-64462: Cryo-EM structure of the Prohibitin complex from Chaetomium therm... -

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Basic information

Entry
Database: EMDB / ID: EMD-64462
TitleCryo-EM structure of the Prohibitin complex from Chaetomium thermophilum
Map data
Sample
  • Complex: the PHB complex from Chaetomium thermophilum
    • Protein or peptide: Prohibitin
    • Protein or peptide: Prohibitin
KeywordsScaffold / SPFH family / MEMBRANE PROTEIN
Function / homology
Function and homology information


mitochondrial prohibitin complex / mitophagy / mitochondrion organization
Similarity search - Function
Prohibitin / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Prohibitin / Prohibitin
Similarity search - Component
Biological speciesChaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) / Thermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLuo DY / Zheng LQ / Lu MA / Chen ZY / Wang PP / Guo Q / Gao N
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92354306 China
CitationJournal: To Be Published
Title: Structural basis for prohibitin-mediated regulation of mitochondrial m-AAA protease
Authors: Luo DY / Zheng LQ / Lu MA / Chen ZY / Wang PP / Guo Q / Gao N
History
DepositionApr 30, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64462.png

Downloads & links

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Map

FileDownload / File: emd_64462.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 280 pix.
= 294.56 Å		1.05 Å/pix.
x 280 pix.
= 294.56 Å		1.05 Å/pix.
x 280 pix.
= 294.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.07869169 - 0.11137273
Average (Standard dev.)0.00046254552 (±0.0060239146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 294.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64462_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_64462_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_64462_half_map_2.map
Projections & Slices
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Sample components

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Entire : the PHB complex from Chaetomium thermophilum

EntireName: the PHB complex from Chaetomium thermophilum
Components
  • Complex: the PHB complex from Chaetomium thermophilum
    • Protein or peptide: Prohibitin
    • Protein or peptide: Prohibitin

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Supramolecule #1: the PHB complex from Chaetomium thermophilum

SupramoleculeName: the PHB complex from Chaetomium thermophilum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Macromolecule #1: Prohibitin

MacromoleculeName: Prohibitin / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 28.503582 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: FIYQAAVPAA VGVGLLQASM YDVKGGTRAV IFDRLSGVKE QVVNEGTHFL IPWLQKAIIF DVRTKPRIIP TTTGSKDLQM VSLTLRVLH RPEVQALPKI YQNLGTDYDE RVLPSIGNEV LKAIVAQYDA AELITQREVV SQRIRHDLTK RAREFNIALE D VSITHLTF ...String:
FIYQAAVPAA VGVGLLQASM YDVKGGTRAV IFDRLSGVKE QVVNEGTHFL IPWLQKAIIF DVRTKPRIIP TTTGSKDLQM VSLTLRVLH RPEVQALPKI YQNLGTDYDE RVLPSIGNEV LKAIVAQYDA AELITQREVV SQRIRHDLTK RAREFNIALE D VSITHLTF GKEFTKAVEQ KQIAQQDAER ARFIVERAEQ ERQANVIRAE GEAEAAETIS KAIAKAGDGL IQIRRLEASR EI AQTLANN PNVVYLPGG

UniProtKB: Prohibitin

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Macromolecule #2: Prohibitin

MacromoleculeName: Prohibitin / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 29.437846 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: ATLMLLGGTA FVFNSCLFNV EGGHRAIKYR RISGVSKDIY GEGTHFMIPW FETPIIYDVR AKPRNVSSLT GTKDLQMVNI TCRVLSRPD IQALPQIYRT LGLDYDERVL PSIVNEVLKA VVAQFNASQL ITQREMVARL VRENLAGRAA RFNILLDDVS L THLAFSPE ...String:
ATLMLLGGTA FVFNSCLFNV EGGHRAIKYR RISGVSKDIY GEGTHFMIPW FETPIIYDVR AKPRNVSSLT GTKDLQMVNI TCRVLSRPD IQALPQIYRT LGLDYDERVL PSIVNEVLKA VVAQFNASQL ITQREMVARL VRENLAGRAA RFNILLDDVS L THLAFSPE FTAAVEAKQV AQQEAQRAAF IVDKARQEKQ ATVVKAQGEA RAAELIGEAI KKNKAYVELK KLENARVIAQ LL QESGKNR LLLDSEGLGL NVFEDQE

UniProtKB: Prohibitin

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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

BufferpH: 7.6
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 2900 / Average electron dose: 52.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C11 (11 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 10623
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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