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- EMDB-27899: Cryo-EM structure of human glycerol-3-phosphate acyltransferase 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-27899
TitleCryo-EM structure of human glycerol-3-phosphate acyltransferase 1 (GPAT1) in complex with CoA and palmitoyl-LPA
Map dataHalf map 1
Sample
  • Complex: glycerol-3-phosphate acyltransferase 1
    • Protein or peptide: Glycerol-3-phosphate acyltransferase 1, mitochondrial
  • Ligand: COENZYME A
  • 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 / activation-induced cell death of T cells / acyl-CoA metabolic process / phospholipid homeostasis / positive regulation of multicellular organism growth / activated T cell proliferation / 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: 3.67 Å
AuthorsWasilko DJ / Johnson ZL / 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: Johnson ZL / Ammirati M / Wasilko DJ / Chang JS / Noell S / Foley TL / Yoon H / Smith K / Asano S / Hales K / Wan M / Yang Q / Piotrowski MA / Farley KA / Gilbert T / Aschenbrenner LM / ...Authors: Johnson ZL / Ammirati M / Wasilko DJ / Chang JS / Noell S / Foley TL / Yoon H / Smith K / Asano S / Hales K / Wan M / Yang Q / Piotrowski MA / Farley KA / Gilbert T / Aschenbrenner LM / Fennell KF / Dutra JK / Xu M / Guo C / Varghese AE / Bellenger J / Quinn A / Am Ende CW / West GM / Griffor MC / Bennett D / Calabrese M / Steppan CM / Han S / Wu H
History
DepositionAug 19, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_27899.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHalf map 1
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.05541692 - 0.10193918
Average (Standard dev.)0.000010023016 (±0.0020905666)
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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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: COENZYME A
  • 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: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 2 / Number of copies: 1 / Formula: COA
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
COENZYME A

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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

Concentration6.1 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
150.0 uMpalmitoyl-LPA
1.0 mMCoA
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: 1 / Number real images: 9153 / Average exposure time: 9.0 sec. / Average electron dose: 78.0 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: 1704123
Startup modelType of model: EMDB MAP
EMDB ID:

27898


Details: GPAT1 2-oxohexadecyl-CoA structure
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 76033
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1.2)

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Atomic model buiding 1

Initial modelPDB ID:

8e4y


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

PDB-8e50:
Cryo-EM structure of human glycerol-3-phosphate acyltransferase 1 (GPAT1) in complex with CoA and palmitoyl-LPA

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