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- PDB-8hf3: Cryo-EM structure of human ZDHHC9/GCP16 complex -

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Basic information

Entry
Database: PDB / ID: 8hf3
TitleCryo-EM structure of human ZDHHC9/GCP16 complex
Components
  • Golgin subfamily A member 7
  • Palmitoyltransferase ZDHHC9
KeywordsTRANSFERASE / plamitoytransferase / palmitoylation / DHHC / RAS
Function / homology
Function and homology information


Ras palmitoyltransferase activity / palmitoyltransferase complex / peptidyl-L-cysteine S-palmitoylation / protein palmitoylation / protein S-acyltransferase / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / positive regulation of pyroptotic inflammatory response / Golgi to plasma membrane transport / positive regulation of cGAS/STING signaling pathway ...Ras palmitoyltransferase activity / palmitoyltransferase complex / peptidyl-L-cysteine S-palmitoylation / protein palmitoylation / protein S-acyltransferase / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / positive regulation of pyroptotic inflammatory response / Golgi to plasma membrane transport / positive regulation of cGAS/STING signaling pathway / host-mediated activation of viral process / Golgi to plasma membrane protein transport / Golgi stack / protein targeting to membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / RAS processing / tertiary granule lumen / MAPK cascade / Maturation of spike protein / protein stabilization / Golgi membrane / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome / extracellular region / cytosol
Similarity search - Function
: / Golgin subfamily A member 7/ERF4 / Golgin subfamily A member 7/ERF4 family / Palmitoyltransferase ZDHHC16 / Palmitoyltransferase, DHHC domain / DHHC palmitoyltransferase / DHHC domain profile.
Similarity search - Domain/homology
PALMITIC ACID / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / Golgin subfamily A member 7 / Palmitoyltransferase ZDHHC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWu, J. / Hu, Q. / Zhang, Y. / Liu, S. / Yang, A.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Regulation of RAS palmitoyltransferases by accessory proteins and palmitoylation.
Authors: Anlan Yang / Shengjie Liu / Yuqi Zhang / Jia Chen / Yujing Fan / Fengxiang Wang / Yilong Zou / Shan Feng / Jianping Wu / Qi Hu /
Abstract: Palmitoylation of cysteine residues at the C-terminal hypervariable regions in human HRAS and NRAS, which is necessary for RAS signaling, is catalyzed by the acyltransferase DHHC9 in complex with its ...Palmitoylation of cysteine residues at the C-terminal hypervariable regions in human HRAS and NRAS, which is necessary for RAS signaling, is catalyzed by the acyltransferase DHHC9 in complex with its accessory protein GCP16. The molecular basis for the acyltransferase activity and the regulation of DHHC9 by GCP16 is not clear. Here we report the cryo-electron microscopy structures of the human DHHC9-GCP16 complex and its yeast counterpart-the Erf2-Erf4 complex, demonstrating that GCP16 and Erf4 are not directly involved in the catalytic process but stabilize the architecture of DHHC9 and Erf2, respectively. We found that a phospholipid binding to an arginine-rich region of DHHC9 and palmitoylation on three residues (C24, C25 and C288) were essential for the catalytic activity of the DHHC9-GCP16 complex. Moreover, we showed that GCP16 also formed complexes with DHHC14 and DHHC18 to catalyze RAS palmitoylation. These findings provide insights into the regulatory mechanism of RAS palmitoyltransferases.
History
DepositionNov 9, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.0Nov 22, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
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Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.3Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Palmitoyltransferase ZDHHC9
B: Golgin subfamily A member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4509
Polymers58,7582
Non-polymers1,6927
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Palmitoyltransferase ZDHHC9 / Zinc finger DHHC domain-containing protein 9 / DHHC-9 / DHHC9 / Zinc finger protein 379 / Zinc ...Zinc finger DHHC domain-containing protein 9 / DHHC-9 / DHHC9 / Zinc finger protein 379 / Zinc finger protein 380


Mass: 41954.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ZDHHC9, CXorf11, ZDHHC10, ZNF379, ZNF380, CGI-89, UNQ261/PRO298
Production host: Homo sapiens (human) / References: UniProt: Q9Y397, protein S-acyltransferase
#2: Protein Golgin subfamily A member 7 / Golgi complex-associated protein of 16 kDa


Mass: 16803.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOLGA7, GCP16, HDCKB03P, HSPC041 / Production host: Homo sapiens (human) / References: UniProt: Q7Z5G4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H52O8P
Has ligand of interestY
Has protein modificationY

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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: Human ZDHHC9/GCP16 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236435 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0063538
ELECTRON MICROSCOPYf_angle_d0.6714762
ELECTRON MICROSCOPYf_dihedral_angle_d10.192537
ELECTRON MICROSCOPYf_chiral_restr0.043525
ELECTRON MICROSCOPYf_plane_restr0.004594

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