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- PDB-9urz: Cryo-EM structure of the Prohibitin complex from Chaetomium therm... -

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Basic information

Entry
Database: PDB / ID: 9urz
TitleCryo-EM structure of the Prohibitin complex from Chaetomium thermophilum
Components(Prohibitin) x 2
KeywordsMEMBRANE PROTEIN / Scaffold / SPFH family
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 speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLuo, D.Y. / Zheng, L.Q. / Lu, M.A. / Chen, Z.Y. / Wang, P.P. / Guo, Q. / Gao, N.
Funding support China, 1items
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, D.Y. / Zheng, L.Q. / Lu, M.A. / Chen, Z.Y. / Wang, P.P. / Guo, Q. / Gao, N.
History
DepositionApr 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)637,35622
Polymers637,35622
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


Mass: 28503.582 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063420 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0SEE1
#2: Protein
Prohibitin


Mass: 29437.846 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0057460 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0SCJ5
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: the PHB complex from Chaetomium thermophilum / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 52.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2900
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2PHENIX1.20.1_4487model refinement
5Gctf1.06CTF correction
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C11 (11 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10623 / Symmetry type: POINT

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