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- EMDB-27898: Cryo-EM structure of human glycerol-3-phosphate acyltransferase 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-27898
TitleCryo-EM structure of human glycerol-3-phosphate acyltransferase 1 (GPAT1) in complex with 2-oxohexadecyl-CoA
Map dataSharpened Full Map
Sample
  • Complex: glycerol-3-phosphate acyltransferase 1
    • Protein or peptide: Glycerol-3-phosphate acyltransferase 1, mitochondrial
  • Ligand: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(2-oxohexadecyl)sulfanyl]ethyl}amino)propyl]amino}butyl dihydrogen diphosphate (non-preferred name)
  • Ligand: (2R)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate
Keywordsacyltransferase / LPA / monotopic / mitochondrial / membrane protein
Function / homology
Function and homology information


glycerol-3-phosphate 1-O-acyltransferase / glycerol-3-phosphate O-acyltransferase activity / phosphatidylglycerol biosynthetic process / CDP-diacylglycerol biosynthetic process / Triglyceride biosynthesis / negative regulation of activation-induced cell death of T cells / diacylglycerol biosynthetic process / triglyceride biosynthetic process / glycerophospholipid metabolic process / phosphatidic acid biosynthetic process ...glycerol-3-phosphate 1-O-acyltransferase / glycerol-3-phosphate O-acyltransferase activity / phosphatidylglycerol biosynthetic process / CDP-diacylglycerol biosynthetic process / Triglyceride biosynthesis / negative regulation of activation-induced cell death of T cells / diacylglycerol biosynthetic process / triglyceride biosynthetic process / glycerophospholipid metabolic process / phosphatidic acid biosynthetic process / Synthesis of PA / acyl-CoA metabolic process / phospholipid homeostasis / activated T cell proliferation / positive regulation of multicellular organism growth / activation-induced cell death of T cells / RUNX1 regulates estrogen receptor mediated transcription / positive regulation of activated T cell proliferation / fatty acid homeostasis / response to glucose / regulation of cytokine production / Activation of gene expression by SREBF (SREBP) / fatty acid metabolic process / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / defense response to virus / Estrogen-dependent gene expression / mitochondrial outer membrane / mitochondrion / plasma membrane
Similarity search - Function
Glycerol-3-phosphate O-acyltransferase/Dihydroxyacetone phosphate acyltransferase / Glycerol-3-phosphate acyltransferase, PlsB / GPAT/DHAPAT, acyltransferase domain / GPAT/DHAPAT, C-terminal domain / Glycerol-3-phosphate acyltransferase C-terminal region / Phospholipid/glycerol acyltransferase / Acyltransferase / Phosphate acyltransferases
Similarity search - Domain/homology
Glycerol-3-phosphate acyltransferase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJohnson ZL / Wasilko DJ / Ammirati M / Chang JS / Han S / Wu H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structural basis of the acyl-transfer mechanism of human GPAT1.
Authors: Zachary Lee Johnson / Mark Ammirati / David Jonathan Wasilko / Jeanne S Chang / Stephen Noell / Timothy L Foley / Hyejin Yoon / Kathleen Smith / Shoh Asano / Katherine Hales / Min Wan / ...Authors: Zachary Lee Johnson / Mark Ammirati / David Jonathan Wasilko / Jeanne S Chang / Stephen Noell / Timothy L Foley / Hyejin Yoon / Kathleen Smith / Shoh Asano / Katherine Hales / Min Wan / Qingyi Yang / Mary A Piotrowski / Kathleen A Farley / Tamara Gilbert / Lisa M Aschenbrenner / Kimberly F Fennell / Jason K Dutra / Mary Xu / Chunyang Guo / Alison E Varghese / Justin Bellenger / Alandra Quinn / Christopher W Am Ende / Graham M West / Matthew C Griffor / Donald Bennett / Matthew Calabrese / Claire M Steppan / Seungil Han / Huixian Wu /
Abstract: Glycerol-3-phosphate acyltransferase (GPAT)1 is a mitochondrial outer membrane protein that catalyzes the first step of de novo glycerolipid biosynthesis. Hepatic expression of GPAT1 is linked to ...Glycerol-3-phosphate acyltransferase (GPAT)1 is a mitochondrial outer membrane protein that catalyzes the first step of de novo glycerolipid biosynthesis. Hepatic expression of GPAT1 is linked to liver fat accumulation and the severity of nonalcoholic fatty liver diseases. Here we present the cryo-EM structures of human GPAT1 in substrate analog-bound and product-bound states. The structures reveal an N-terminal acyltransferase domain that harbors important catalytic motifs and a tightly associated C-terminal domain that is critical for proper protein folding. Unexpectedly, GPAT1 has no transmembrane regions as previously proposed but instead associates with the membrane via an amphipathic surface patch and an N-terminal loop-helix region that contains a mitochondrial-targeting signal. Combined structural, computational and functional studies uncover a hydrophobic pathway within GPAT1 for lipid trafficking. The results presented herein lay a framework for rational inhibitor development for GPAT1.
History
DepositionAug 19, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27898.png

Downloads & links

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Map

FileDownload / File: emd_27898.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Full Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.056053016 - 0.104565546
Average (Standard dev.)0.000041592273 (±0.0021437758)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map

Fileemd_27898_half_map_1.map
AnnotationHalf Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map

Fileemd_27898_half_map_2.map
AnnotationHalf Map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : glycerol-3-phosphate acyltransferase 1

EntireName: glycerol-3-phosphate acyltransferase 1
Components
  • Complex: glycerol-3-phosphate acyltransferase 1
    • Protein or peptide: Glycerol-3-phosphate acyltransferase 1, mitochondrial
  • Ligand: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(2-oxohexadecyl)sulfanyl]ethyl}amino)propyl]amino}butyl dihydrogen diphosphate (non-preferred name)
  • Ligand: (2R)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate

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Supramolecule #1: glycerol-3-phosphate acyltransferase 1

SupramoleculeName: glycerol-3-phosphate acyltransferase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86 KDa

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Macromolecule #1: Glycerol-3-phosphate acyltransferase 1, mitochondrial

MacromoleculeName: Glycerol-3-phosphate acyltransferase 1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: glycerol-3-phosphate 1-O-acyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.919469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKG SENLYFQSNP SIPSLGLRNV IYINETHTRH RGWLARRLSY VLFIQERDVH KGMFATNVTE NVLNSSRVQE AIAEVAAEL NPDGSAQQQS KAVNKVKKKA KRILQEMVAT VSPAMIRLTG WVLLKLFNSF FWNIQIHKGQ LEMVKAATET N LPLLFLPV ...String:
MDYKDDDDKG SENLYFQSNP SIPSLGLRNV IYINETHTRH RGWLARRLSY VLFIQERDVH KGMFATNVTE NVLNSSRVQE AIAEVAAEL NPDGSAQQQS KAVNKVKKKA KRILQEMVAT VSPAMIRLTG WVLLKLFNSF FWNIQIHKGQ LEMVKAATET N LPLLFLPV HRSHIDYLLL TFILFCHNIK APYIASGNNL NIPIFSTLIH KLGGFFIRRR LDETPDGRKD VLYRALLHGH IV ELLRQQQ FLEIFLEGTR SRSGKTSCAR AGLLSVVVDT LSTNVIPDIL IIPVGISYDR IIEGHYNGEQ LGKPKKNESL WSV ARGVIR MLRKNYGCVR VDFAQPFSLK EYLESQSQKP VSALLSLEQA LLPAILPSRP SDAADEGRDT SINESRNATD ESLR RRLIA NLAEHILFTA SKSCAIMSTH IVACLLLYRH RQGIDLSTLV EDFFVMKEEV LARDFDLGFS GNSEDVVMHA IQLLG NCVT ITHTSRNDEF FITPSTTVPS VFELNFYSNG VLHVFIMEAI IACSLYAVLN KRGLGGPTST PPNLISQEQL VRKAAS LCY LLSNEGTISL PCQTFYQVCH ETVGKFIQYG ILTVAEHDDQ EDISPSLAEQ QWDKKLPEPL SWRSDEEDED SDFGEEQ RD CYLKVSQSKE HQQFITFLQR LLGPLLEAYS SAAIFVHNFS GPVPEPEYLQ KLHKYLITRT ERNVAVYAES ATYCLVKN A VKMFKDIGVF KETKQKRVSV LELSSTFLPQ CNRQKLLEYI LSFVVL

UniProtKB: Glycerol-3-phosphate acyltransferase 1, mitochondrial

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Macromolecule #2: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonoox...

MacromoleculeName: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(2-oxohexadecyl)sulfanyl]ethyl}amino)propyl]amino}butyl ...Name: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(2-oxohexadecyl)sulfanyl]ethyl}amino)propyl]amino}butyl dihydrogen diphosphate (non-preferred name)
type: ligand / ID: 2 / Number of copies: 1 / Formula: UKL
Molecular weightTheoretical: 1.005943 KDa
Chemical component information

ChemComp-UKL:
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(2-oxohexadecyl)sulfanyl]ethyl}amino)propyl]amino}butyl dihydrogen diphosphate (non-preferred name)

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Macromolecule #3: (2R)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate

MacromoleculeName: (2R)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate / type: ligand / ID: 3 / Number of copies: 1 / Formula: NKO
Molecular weightTheoretical: 410.483 Da
Chemical component information

ChemComp-NKO:
(2R)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate

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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

Concentration5.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
50.0 mMHEPES
150.0 mMSodium Chloride
0.06 PercentDigitonin
1.0 mMDTT
3.0 mMfluorinated Fos-Choline-8
100.0 uM2-oxohexadacyl CoA
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force -5, blot time 3 sec.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 2 / Number real images: 8491 / Average exposure time: 7.0 sec. / Average electron dose: 74.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailscollected in super resolution mode; gain normalized and binned by 2 during motion correction
Particle selectionNumber selected: 1721277
Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated in Relion 3.0.5 from subset of data
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 161511
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1k30


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8e4y:
Cryo-EM structure of human glycerol-3-phosphate acyltransferase 1 (GPAT1) in complex with 2-oxohexadecyl-CoA

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