[English] 日本語
Yorodumi
- PDB-8hf3: Cryo-EM structure of human ZDHHC9/GCP16 complex -

+
Open data


ID or keywords:

Loading...

-
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


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 / Neutrophil degranulation / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / cytosol
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
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 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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

-
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)

-
Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: 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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more