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- EMDB-38375: Structure of acyltransferase GWT1 in complex with manogepix(APX001A) -

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Basic information

Entry
Database: EMDB / ID: EMD-38375
TitleStructure of acyltransferase GWT1 in complex with manogepix(APX001A)
Map data
Sample
  • Complex: Complex of GWT1 and inhibitor APX001A
    • Protein or peptide: GPI-anchored wall transfer protein 1
  • Ligand: 3-[3-[[4-(pyridin-2-yloxymethyl)phenyl]methyl]-1,2-oxazol-5-yl]pyridin-2-amine
Keywordsacyltransferase / MEMBRANE PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


glucosaminyl-phosphatidylinositol O-acyltransferase activity / Synthesis of glycosylphosphatidylinositol (GPI) / Transferases; Acyltransferases / GPI anchor biosynthetic process / nuclear outer membrane-endoplasmic reticulum membrane network / protein localization to plasma membrane / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
Phosphatidylinositol anchor biosynthesis protein PIGW/GWT1 / GWT1
Similarity search - Domain/homology
GPI-anchored wall transfer protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsDai XL / Li JL / Liu XZ / Deng D / Wang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Structural insights into the inhibition mechanism of fungal GWT1 by manogepix
Authors: Dai X / Liu X / Li J / Chen H / Yan C / Li Y / Liu H / Deng D / Wang X
History
DepositionDec 19, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38375.png

Downloads & links

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Map

FileDownload / File: emd_38375.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.1367097 - 1.5315496
Average (Standard dev.)0.0009143286 (±0.024956567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38375_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38375_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38375_half_map_2.map
Projections & Slices
AxesZYX

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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 : Complex of GWT1 and inhibitor APX001A

EntireName: Complex of GWT1 and inhibitor APX001A
Components
  • Complex: Complex of GWT1 and inhibitor APX001A
    • Protein or peptide: GPI-anchored wall transfer protein 1
  • Ligand: 3-[3-[[4-(pyridin-2-yloxymethyl)phenyl]methyl]-1,2-oxazol-5-yl]pyridin-2-amine

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Supramolecule #1: Complex of GWT1 and inhibitor APX001A

SupramoleculeName: Complex of GWT1 and inhibitor APX001A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: GPI-anchored wall transfer protein 1

MacromoleculeName: GPI-anchored wall transfer protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Transferases; Acyltransferases
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 55.511918 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTLKQRKED FVTGLNGGSI TEINAVTSIA LVTYISWNLL KNSNLMPPGI SSVQYIIDFA LNWVALLLSI TIYASEPYLL NTLILLPCL LAFIYGKFTS SSKPSNPIYN KKKMITQRFQ LEKKPYITAY RGGMLILTAI AILAVDFPIF PRRFAKVETW G TSLMDLGV ...String:
MSTLKQRKED FVTGLNGGSI TEINAVTSIA LVTYISWNLL KNSNLMPPGI SSVQYIIDFA LNWVALLLSI TIYASEPYLL NTLILLPCL LAFIYGKFTS SSKPSNPIYN KKKMITQRFQ LEKKPYITAY RGGMLILTAI AILAVDFPIF PRRFAKVETW G TSLMDLGV GSFVFSNGIV SSRALLKNLS LKSKPSFLKN AFNALKSGGT LLFLGLLRLF FVKNLEYQEH VTEYGVHWNF FI TLSLLPL VLTFIDPVTR MVPRCSIAIF ISCIYEWLLL KDDRTLNFLI LADRNCFFSA NREGIFSFLG YCSIFLWGQN TGF YLLGNK PTLNNLYKPS TQDVVAASKK SSTWDYWTSV TPLSGLCIWS TIFLVISQLV FQYHPYSVSR RFANLPYTLW VITY NLLFL TGYCLTDKIF GNSSEYYKVA ECLESINSNG LFLFLLANVS TGLVNMSMVT IDSSPLKSFL VLLAYCSFIA VISVF LYRK RIFIKL

UniProtKB: GPI-anchored wall transfer protein 1

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Macromolecule #2: 3-[3-[[4-(pyridin-2-yloxymethyl)phenyl]methyl]-1,2-oxazol-5-yl]py...

MacromoleculeName: 3-[3-[[4-(pyridin-2-yloxymethyl)phenyl]methyl]-1,2-oxazol-5-yl]pyridin-2-amine
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1LVI
Molecular weightTheoretical: 358.393 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 252957
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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