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- EMDB-34711: Cryo-EM structure of human ZDHHC9/GCP16 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-34711
TitleCryo-EM structure of human ZDHHC9/GCP16 complex
Map datathe refined map of human DHHC9/GCP16 complex
Sample
  • Complex: Human ZDHHC9/GCP16 complex
    • Protein or peptide: Palmitoyltransferase ZDHHC9
    • Protein or peptide: Golgin subfamily A member 7
  • Ligand: ZINC ION
  • Ligand: PALMITIC ACID
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
Keywordsplamitoytransferase / palmitoylation / DHHC / RAS / TRANSFERASE
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
Golgin subfamily A member 7 / Palmitoyltransferase ZDHHC9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWu J / Hu Q / Zhang Y / Liu S / Yang A
Funding support China, 1 items
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, 2022-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34711.png

Downloads & links

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Map

FileDownload / File: emd_34711.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe refined map of human DHHC9/GCP16 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.758 Å		0.84 Å/pix.
x 256 pix.
= 214.758 Å		0.84 Å/pix.
x 256 pix.
= 214.758 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8389 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-3.6980543 - 5.4847965
Average (Standard dev.)0.0025120447 (±0.091234505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.7584 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: the half A map of human DHHC9/GCP16 complex

Fileemd_34711_half_map_1.map
Annotationthe half A map of human DHHC9/GCP16 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: the half B map of human DHHC9/GCP16 complex

Fileemd_34711_half_map_2.map
Annotationthe half B map of human DHHC9/GCP16 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human ZDHHC9/GCP16 complex

EntireName: Human ZDHHC9/GCP16 complex
Components
  • Complex: Human ZDHHC9/GCP16 complex
    • Protein or peptide: Palmitoyltransferase ZDHHC9
    • Protein or peptide: Golgin subfamily A member 7
  • Ligand: ZINC ION
  • Ligand: PALMITIC ACID
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

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Supramolecule #1: Human ZDHHC9/GCP16 complex

SupramoleculeName: Human ZDHHC9/GCP16 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Palmitoyltransferase ZDHHC9

MacromoleculeName: Palmitoyltransferase ZDHHC9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein S-acyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.954457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSVMVVRKKV TRKWEKLPGR NTFCCDGRVM MARQKGIFYL TLFLILGTCT LFFAFECRYL AVQLSPAIPV FAAMLFLFSM ATLLRTSFS DPGVIPRALP DEAAFIEMEI EATNGAVPQG QRPPPRIKNF QINNQIVKLK YCYTCKIFRP PRASHCSICD N CVERFDHH ...String:
MSVMVVRKKV TRKWEKLPGR NTFCCDGRVM MARQKGIFYL TLFLILGTCT LFFAFECRYL AVQLSPAIPV FAAMLFLFSM ATLLRTSFS DPGVIPRALP DEAAFIEMEI EATNGAVPQG QRPPPRIKNF QINNQIVKLK YCYTCKIFRP PRASHCSICD N CVERFDHH CPWVGNCVGK RNYRYFYLFI LSLSLLTIYV FAFNIVYVAL KSLKIGFLET LKETPGTVLE VLICFFTLWS VV GLTGFHT FLVALNQTTN EDIKGSWTGK NRVQNPYSHG NIVKNCCEVL CGPLPPSVLD RRGILPLEES GSRPPSTQET SSS LLPQSP APTEHLNSNE MPEDSSTPEE MPPPEPPEPP QEAAEAEKDY KDDDDK

UniProtKB: Palmitoyltransferase ZDHHC9

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Macromolecule #2: Golgin subfamily A member 7

MacromoleculeName: Golgin subfamily A member 7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.803133 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MHHHHHHMRP QQAPVSGKVF IQRDYSSGTR CQFQTKFPAE LENRIDRQQF EETVRTLNNL YAEAEKLGGQ SYLEGCLACL TAYTIFLCM ETHYEKVLKK VSKYIQEQNE KIYAPQGLLL TDPIERGLRV IEITIYEDRG MSSGR

UniProtKB: Golgin subfamily A member 7

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #5: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: PX2
Molecular weightTheoretical: 535.671 Da
Chemical component information

ChemComp-PX2:
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 236435
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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