+Open data
-Basic information
Entry | Database: PDB / ID: 8hfc | ||||||
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Title | Cryo-EM structure of yeast Erf2/Erf4 complex | ||||||
Components |
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Keywords | TRANSFERASE / palmitoyltransferase / Saccaromyces cerevisiae / palmitoylation / RAS2 | ||||||
Function / homology | Function and homology information endoplasmic reticulum palmitoyltransferase complex / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / protein targeting to membrane / Neutrophil degranulation / endoplasmic reticulum membrane ...endoplasmic reticulum palmitoyltransferase complex / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / protein targeting to membrane / Neutrophil degranulation / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Wu, J. / Hu, Q. / Zhang, Y. / Yang, A. / Liu, S. | ||||||
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 | 8hfc.cif.gz | 106.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hfc.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 8hfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/8hfc ftp://data.pdbj.org/pub/pdb/validation_reports/hf/8hfc | HTTPS FTP |
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-Related structure data
Related structure data | 34717MC 8hf3C 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: 43811.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: ERF2, YLR246W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q06551, protein S-acyltransferase | ||
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#2: Protein | Mass: 29652.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SHR5, ERF4, YOL110W, HRC237 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41912 | ||
#3: Chemical | ChemComp-PLM / | ||
#4: Chemical | 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: Erf2/Erf4 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191610 / Symmetry type: POINT | ||||||||||||||||||||||||
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