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- EMDB-70274: Cryo-EM structure of the Zdhhc5-GOLGA7 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-70274
TitleCryo-EM structure of the Zdhhc5-GOLGA7 complex
Map data
Sample
  • Complex: Zdhhc5/GOLGA7 complex
    • Protein or peptide: Palmitoyltransferase ZDHHC5
    • Protein or peptide: Golgin subfamily A member 7
  • Ligand: ZINC ION
Keywordspalmitoyltransferase membrane protein complex protein S-acylation accessory protein / TRANSFERASE
Function / homology
Function and homology information


positive regulation of protein localization to phagocytic vesicle / palmitoyltransferase complex / peptidyl-L-cysteine S-palmitoylation / positive regulation of pattern recognition receptor signaling pathway / protein S-acyltransferase / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / positive regulation of pyroptotic inflammatory response / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport ...positive regulation of protein localization to phagocytic vesicle / palmitoyltransferase complex / peptidyl-L-cysteine S-palmitoylation / positive regulation of pattern recognition receptor signaling pathway / protein S-acyltransferase / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / positive regulation of pyroptotic inflammatory response / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / Golgi stack / postsynaptic specialization, intracellular component / protein targeting to membrane / lipid transport / positive regulation of NLRP3 inflammasome complex assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / phagocytic vesicle / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / GABA-ergic synapse / RAS processing / tertiary granule lumen / Maturation of spike protein / postsynapse / protein stabilization / Golgi membrane / innate immune response / dendrite / Neutrophil degranulation / glutamatergic synapse / extracellular exosome / extracellular region / nucleoplasm / plasma membrane
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
Golgin subfamily A member 7 / Palmitoyltransferase ZDHHC5
Similarity search - Component
Biological speciesMammalia (mammals) / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKahlson MA / Dixon SJ / Butterwick JA / Wang H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA272485 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007276 United States
CitationJournal: J Biol Chem / Year: 2025
Title: Functional dissection of the zDHHC palmitoyltransferase 5-golgin A7 palmitoylation complex.
Authors: Martha A Kahlson / Joan Ritho / João Victor Gomes / Haoqing Wang / Joel A Butterwick / Scott J Dixon /
Abstract: Small molecules serve as valuable tools for probing nonapoptotic cell death mechanisms. The small molecule caspase independent lethal 56 (CIL56) induces a unique form of nonapoptotic cancer cell ...Small molecules serve as valuable tools for probing nonapoptotic cell death mechanisms. The small molecule caspase independent lethal 56 (CIL56) induces a unique form of nonapoptotic cancer cell death that is promoted by a complex formed between zDHHC palmitoyltransferase 5 (ZDHHC5) and an accessory protein, golgin A7 (GOLGA7, also known as GCP16). The structure and function of this complex in nonapoptotic cell death regulation remain poorly understood. Here, we use coimmunoprecipitation, functional assays, and cryogenic electron microscopy (cryo-EM) to elucidate the structure and function of the Zdhhc5-GOLGA7 complex. We identify key residues in both Zdhhc5 and GOLGA7 that are necessary for complex formation and to promote nonapoptotic cancer cell death in response to caspase independent lethal 56. These results provide new insights into the structure and function of a death-promoting protein complex.
History
DepositionApr 19, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70274.png

Downloads & links

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Map

FileDownload / File: emd_70274.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.6306621 - 1.1839945
Average (Standard dev.)0.0003627257 (±0.010848678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70274_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70274_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Zdhhc5/GOLGA7 complex

EntireName: Zdhhc5/GOLGA7 complex
Components
  • Complex: Zdhhc5/GOLGA7 complex
    • Protein or peptide: Palmitoyltransferase ZDHHC5
    • Protein or peptide: Golgin subfamily A member 7
  • Ligand: ZINC ION

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Supramolecule #1: Zdhhc5/GOLGA7 complex

SupramoleculeName: Zdhhc5/GOLGA7 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Mammalia (mammals)

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Macromolecule #1: Golgin subfamily A member 7

MacromoleculeName: Golgin subfamily A member 7 / type: protein_or_peptide / ID: 1
Details: Full-length human GOLGA7 with N-terminal FLAG tag and flexible linker
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.556865 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDYKDDDDKS GRAMRPQQAP VSGKVFIQRD YSSGTRCQFQ TKFPAELENR IDRQQFEETV RTLNNLYAEA EKLGGQSYLE GCLACLTAY TIFLCMETHY EKVLKKVSKY IQEQNEKIYA PQGLLLTDPI ERGLRVIEIT IYEDRGMSSG RAAA

UniProtKB: Golgin subfamily A member 7

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Macromolecule #2: Palmitoyltransferase ZDHHC5

MacromoleculeName: Palmitoyltransferase ZDHHC5 / type: protein_or_peptide / ID: 2
Details: N-terminal 3xFLAG-sfGFP fusion to full length mouse Zdhhc5 separated by a TEV protease cleavage site and flexible linker
Number of copies: 1 / Enantiomer: LEVO / EC number: protein S-acyltransferase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 77.809891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPAESGKRFK PSKYVPVSAA AIFLVGATTL FFAFTCPGLS LNVSPAVPIY NAIMFLFVLA NFSMATFMDP GIFPRAEEDE DKEDDFRAP LYKTVEIKGI QVRMKWCATC RFYRPPRCSH CSVCDNCVEE FDHHCPWVNN CIGRRNYRYF FLFLLSLTAH I MGVFGFGL ...String:
MPAESGKRFK PSKYVPVSAA AIFLVGATTL FFAFTCPGLS LNVSPAVPIY NAIMFLFVLA NFSMATFMDP GIFPRAEEDE DKEDDFRAP LYKTVEIKGI QVRMKWCATC RFYRPPRCSH CSVCDNCVEE FDHHCPWVNN CIGRRNYRYF FLFLLSLTAH I MGVFGFGL LYVLYHIEEL SGVRTAVTMA VMCVAGLFFI PVAGLTGFHV VLVARGRTTN EQVTGKFRGG VNPFTNGCCN NV SRVLCSS PAPRYLGRPK KEKTIVIRPP FLRPEVSDGQ ITVKIMDNGI QGELRRTKSK GSLEITESQS ADAEPPPPPK PDL SRYTGL RTHLSLATNE DSSLLGKDSP PTPTMYKYRP GYSSSSTSAA MPHSSSAKLS RGDSLKEPTS IADSSRHPSY RSEP SLEPE SFRSPTFGKS FHFDPLSSGS RSSSLKSAQG TGFELGQLQS IRSEGTTSTS YKSLANQTRN GSLSYDSLLT PSDSP DFES VQAGPEPDPP LGYTSPFLSA RLAQQREAER HPRLLPTGPP HREPSPVRYD NLSRHIVASL QEREKLLRQS PPLAGR EEE PGLGDSGIQS TPGSGHAPRT SSSSDDSKRS PLSKTPLGRP AVPRFGKPDG LRSRGLGSPE PGTTAPYLGR SISYSSQ KA PSGVSETEEV ALQPLLTPKD EVQLKTTYSK SNGQPKSIGS ASPGPGQPPL SSPTRGGVKK VSGVGGTTYE ISVAAA

UniProtKB: Palmitoyltransferase ZDHHC5

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 0.2 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1383157
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold 3-predicted model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 93643
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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