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- PDB-9oa6: Cryo-EM structure of the Zdhhc5-GOLGA7 complex -

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Basic information

Entry
Database: PDB / ID: 9oa6
TitleCryo-EM structure of the Zdhhc5-GOLGA7 complex
Components
  • Golgin subfamily A member 7
  • Palmitoyltransferase ZDHHC5
KeywordsTRANSFERASE / palmitoyltransferase membrane protein complex protein S-acylation accessory protein
Function / homology
Function and homology information


positive regulation of protein localization to phagocytic vesicle / palmitoyltransferase complex / peptidyl-L-cysteine S-palmitoylation / positive regulation of pattern recognition receptor signaling pathway / protein S-acyltransferase / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / positive regulation of pyroptotic inflammatory response / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport ...positive regulation of protein localization to phagocytic vesicle / palmitoyltransferase complex / peptidyl-L-cysteine S-palmitoylation / positive regulation of pattern recognition receptor signaling pathway / protein S-acyltransferase / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / positive regulation of pyroptotic inflammatory response / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / Golgi stack / postsynaptic specialization, intracellular component / protein targeting to membrane / lipid transport / positive regulation of NLRP3 inflammasome complex assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / phagocytic vesicle / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / GABA-ergic synapse / RAS processing / tertiary granule lumen / Maturation of spike protein / postsynapse / protein stabilization / Golgi membrane / innate immune response / dendrite / Neutrophil degranulation / glutamatergic synapse / extracellular exosome / extracellular region / nucleoplasm / plasma membrane
Similarity search - Function
: / Golgin subfamily A member 7/ERF4 / Golgin subfamily A member 7/ERF4 family / Palmitoyltransferase, DHHC domain / DHHC palmitoyltransferase / DHHC domain profile.
Similarity search - Domain/homology
Golgin subfamily A member 7 / Palmitoyltransferase ZDHHC5
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKahlson, M.A. / Dixon, S.J. / Butterwick, J.A. / Wang, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA272485 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007276 United States
CitationJournal: J Biol Chem / Year: 2025
Title: Functional dissection of the zDHHC palmitoyltransferase 5-golgin A7 palmitoylation complex.
Authors: Martha A Kahlson / Joan Ritho / João Victor Gomes / Haoqing Wang / Joel A Butterwick / Scott J Dixon /
Abstract: Small molecules serve as valuable tools for probing nonapoptotic cell death mechanisms. The small molecule caspase independent lethal 56 (CIL56) induces a unique form of nonapoptotic cancer cell ...Small molecules serve as valuable tools for probing nonapoptotic cell death mechanisms. The small molecule caspase independent lethal 56 (CIL56) induces a unique form of nonapoptotic cancer cell death that is promoted by a complex formed between zDHHC palmitoyltransferase 5 (ZDHHC5) and an accessory protein, golgin A7 (GOLGA7, also known as GCP16). The structure and function of this complex in nonapoptotic cell death regulation remain poorly understood. Here, we use coimmunoprecipitation, functional assays, and cryogenic electron microscopy (cryo-EM) to elucidate the structure and function of the Zdhhc5-GOLGA7 complex. We identify key residues in both Zdhhc5 and GOLGA7 that are necessary for complex formation and to promote nonapoptotic cancer cell death in response to caspase independent lethal 56. These results provide new insights into the structure and function of a death-promoting protein complex.
History
DepositionApr 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Golgin subfamily A member 7
A: Palmitoyltransferase ZDHHC5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4984
Polymers95,3672
Non-polymers1312
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 Golgin subfamily A member 7 / Golgi complex-associated protein of 16 kDa


Mass: 17556.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Full-length human GOLGA7 with N-terminal FLAG tag and flexible linker
Source: (gene. exp.) Homo sapiens (human) / Gene: GOLGA7, GCP16, HDCKB03P, HSPC041 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q7Z5G4
#2: Protein Palmitoyltransferase ZDHHC5 / Zinc finger DHHC domain-containing protein 5 / DHHC-5


Mass: 77809.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal 3xFLAG-sfGFP fusion to full length mouse Zdhhc5 separated by a TEV protease cleavage site and flexible linker
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zdhhc5, Kiaa1748 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q8VDZ4, protein S-acyltransferase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Zdhhc5/GOLGA7 complex / Type: COMPLEX / Entity ID: #2, #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mammalia (mammals)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3particle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARC4.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1383157
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93643 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032976
ELECTRON MICROSCOPYf_angle_d0.7934032
ELECTRON MICROSCOPYf_dihedral_angle_d5.536406
ELECTRON MICROSCOPYf_chiral_restr0.047448
ELECTRON MICROSCOPYf_plane_restr0.007520

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