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- PDB-9zfr: Mitochondrial Hsp60 from Acanthamoeba castellanii -

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Basic information

Entry
Database: PDB / ID: 9zfr
TitleMitochondrial Hsp60 from Acanthamoeba castellanii
ComponentsChaperonin GroL, putative
KeywordsCHAPERONE / mitochondrial Hsp60 / cryoEM
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / protein refolding / ATP binding
Similarity search - Function
Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Chaperonin GroL, putative
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsFry, M.Y. / Luce, B.E. / Stefely, J.A. / Samuelson, J. / Mootha, V.K. / Chao, L.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2026
Title: Acanthamoeba ATP synthase structure reveals the TCA cycle is tethered to OXPHOS.
Authors: Michelle Y Fry / Bridget E Luce / Jonathan A Stefely / Michael Z Chen / Felicia G Deng / Tiana M Issa / / Sarah E Calvo / John Samuelson / Vamsi K Mootha / Luke H Chao /
Abstract: Oxidative phosphorylation (OXPHOS) is a key metabolic process that couples redox energy to ATP production. While some core OXPHOS complex subunits are found across all domains of life, many have ...Oxidative phosphorylation (OXPHOS) is a key metabolic process that couples redox energy to ATP production. While some core OXPHOS complex subunits are found across all domains of life, many have diverged or expanded across evolution-as seen in the protozoan pathogen Acanthamoeba castellanii. By integrating cryo-electron microscopy of unenriched mitochondrial lysate with mass spectrometry proteomics, we resolved the structures of endogenous mitochondrial ATP synthase (complex V), Hsp60, and respiratory complex III from Acanthamoeba. We capture Acanthamoeba ATP synthase in an IF1-inhibited state and reveal how Acanthamoeba-specific subunits and extensions stabilize the molecular machine, which includes a β subunit extension that interfaces with the peripheral stalk. Additionally, we characterize an active malate dehydrogenase (MDH) dimer structurally integrated within the ATP synthase peripheral stalk, thus revealing a direct protein tether between OXPHOS and the tricarboxylic acid cycle. Together, these findings provide structural insight into lineage-specific adaptations in Acanthamoeba that may tune protozoan metabolism.
History
DepositionDec 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperonin GroL, putative
B: Chaperonin GroL, putative
C: Chaperonin GroL, putative
D: Chaperonin GroL, putative
E: Chaperonin GroL, putative
F: Chaperonin GroL, putative
G: Chaperonin GroL, putative
H: Chaperonin GroL, putative
I: Chaperonin GroL, putative
J: Chaperonin GroL, putative
K: Chaperonin GroL, putative
L: Chaperonin GroL, putative
M: Chaperonin GroL, putative
N: Chaperonin GroL, putative


Theoretical massNumber of molelcules
Total (without water)852,74614
Polymers852,74614
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
Chaperonin GroL, putative


Mass: 60910.426 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Details: ACANB13112 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Variant: wild-type / Strain: Neff / References: UniProt: L8GUV2
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: Acanthamoeba castellanii mitochondrial Hsp60 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: .812 MDa / Experimental value: NO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Buffer solutionpH: 7.9
Buffer component
IDConc.NameBuffer-ID
150 mMHEPES1
2300 mMsodium chloride1
34 mMmagnesium chloride1
420 uMCalcium Chloride1
51 mMDithiothreitol1
60.5 % (w/v)DDM1
SpecimenConc.: 2.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was not purified. Instead it was solved from imaging mitochondrial lysate.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.14 K

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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: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 0.99 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARCv.4.7.0particle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
5cryoSPARCv.4.7.0CTF correctionPatch CTF estimation
10cryoSPARCinitial Euler assignmentab initio reconstruction
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1154 / Symmetry type: POINT
RefinementHighest resolution: 3.76 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00547012
ELECTRON MICROSCOPYf_angle_d0.53963280
ELECTRON MICROSCOPYf_dihedral_angle_d3.5046580
ELECTRON MICROSCOPYf_chiral_restr0.047812
ELECTRON MICROSCOPYf_plane_restr0.0038120

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