+Open data
-Basic information
Entry | Database: PDB / ID: 8hf3 | ||||||
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Title | Cryo-EM structure of human ZDHHC9/GCP16 complex | ||||||
Components |
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Keywords | TRANSFERASE / plamitoytransferase / palmitoylation / DHHC / RAS | ||||||
Function / homology | Function and homology information palmitoyltransferase complex / Ras palmitoyltransferase activity / peptidyl-L-cysteine S-palmitoylation / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / Golgi stack ...palmitoyltransferase complex / Ras palmitoyltransferase activity / peptidyl-L-cysteine S-palmitoylation / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / Golgi stack / positive regulation by host of viral process / protein targeting to membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / RAS processing / MAPK cascade / tertiary granule lumen / Maturation of spike protein / protein stabilization / Golgi membrane / endoplasmic reticulum membrane / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Wu, J. / Hu, Q. / Zhang, Y. / Liu, S. / Yang, A. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hf3.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hf3.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 8hf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hf3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8hf3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8hf3_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 8hf3_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/8hf3 ftp://data.pdbj.org/pub/pdb/validation_reports/hf/8hf3 | HTTPS FTP |
-Related structure data
Related structure data | 34711MC 8hfcC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | ||||||
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#2: Protein | 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 | #4: Chemical | ChemComp-PLM / #5: Chemical | ChemComp-PX2 / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human ZDHHC9/GCP16 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236435 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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