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- EMDB-38217: Human GPR34 -Gi complex bound to S3E-LysoPS, receptor focused -

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Basic information

Entry
Database: EMDB / ID: EMD-38217
TitleHuman GPR34 -Gi complex bound to S3E-LysoPS, receptor focused
Map data
Sample
  • Complex: Human GPR34-Gi complex bound to S3E-LysoPS, receptor focused
    • Protein or peptide: Probable G-protein coupled receptor 34
  • Ligand: (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[(~{Z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid
KeywordsGPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


G protein-coupled purinergic nucleotide receptor activity / G protein-coupled receptor activity / G protein-coupled receptor signaling pathway / plasma membrane
Similarity search - Function
: / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Probable G-protein coupled receptor 34
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsKawahara R / Shihoya W / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05037 Japan
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for lysophosphatidylserine recognition by GPR34.
Authors: Tamaki Izume / Ryo Kawahara / Akiharu Uwamizu / Luying Chen / Shun Yaginuma / Jumpei Omi / Hiroki Kawana / Fengjue Hou / Fumiya K Sano / Tatsuki Tanaka / Kazuhiro Kobayashi / Hiroyuki H ...Authors: Tamaki Izume / Ryo Kawahara / Akiharu Uwamizu / Luying Chen / Shun Yaginuma / Jumpei Omi / Hiroki Kawana / Fengjue Hou / Fumiya K Sano / Tatsuki Tanaka / Kazuhiro Kobayashi / Hiroyuki H Okamoto / Yoshiaki Kise / Tomohiko Ohwada / Junken Aoki / Wataru Shihoya / Osamu Nureki /
Abstract: GPR34 is a recently identified G-protein coupled receptor, which has an immunomodulatory role and recognizes lysophosphatidylserine (LysoPS) as a putative ligand. Here, we report cryo-electron ...GPR34 is a recently identified G-protein coupled receptor, which has an immunomodulatory role and recognizes lysophosphatidylserine (LysoPS) as a putative ligand. Here, we report cryo-electron microscopy structures of human GPR34-G complex bound with one of two ligands bound: either the LysoPS analogue S3E-LysoPS, or M1, a derivative of S3E-LysoPS in which oleic acid is substituted with a metabolically stable aromatic fatty acid surrogate. The ligand-binding pocket is laterally open toward the membrane, allowing lateral entry of lipidic agonists into the cavity. The amine and carboxylate groups of the serine moiety are recognized by the charged residue cluster. The acyl chain of S3E-LysoPS is bent and fits into the L-shaped hydrophobic pocket in TM4-5 gap, and the aromatic fatty acid surrogate of M1 fits more appropriately. Molecular dynamics simulations further account for the LysoPS-regioselectivity of GPR34. Thus, using a series of structural and physiological experiments, we provide evidence that chemically unstable 2-acyl LysoPS is the physiological ligand for GPR34. Overall, we anticipate the present structures will pave the way for development of novel anticancer drugs that specifically target GPR34.
History
DepositionDec 6, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38217.png

Downloads & links

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Map

FileDownload / File: emd_38217.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.117 Å
Density
Contour LevelBy AUTHOR: 1.4
Minimum - Maximum-8.605466 - 11.3398
Average (Standard dev.)-0.023626471 (±0.46361813)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin608060
Dimensions969892
Spacing989692
CellA: 109.465996 Å / B: 107.231995 Å / C: 102.764 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38217_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Half map: #2

Fileemd_38217_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38217_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human GPR34-Gi complex bound to S3E-LysoPS, receptor focused

EntireName: Human GPR34-Gi complex bound to S3E-LysoPS, receptor focused
Components
  • Complex: Human GPR34-Gi complex bound to S3E-LysoPS, receptor focused
    • Protein or peptide: Probable G-protein coupled receptor 34
  • Ligand: (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[(~{Z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid

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Supramolecule #1: Human GPR34-Gi complex bound to S3E-LysoPS, receptor focused

SupramoleculeName: Human GPR34-Gi complex bound to S3E-LysoPS, receptor focused
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Probable G-protein coupled receptor 34

MacromoleculeName: Probable G-protein coupled receptor 34 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.702742 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAMG RSHTITMTTT SVSSWPYSSH RMRFITNHSD QPPQNFSATP NVTTCPMDEK LLSTVLTTSY SVIFIVGLVG NIIALYVFL GIHRKRNSIQ IYLLNVAIAD LLLIFCLPFR IMYHINQNKW TLGVILCKVV GTLFYMNMYI SIILLGFISL D RYIKINRS ...String:
DYKDDDDAMG RSHTITMTTT SVSSWPYSSH RMRFITNHSD QPPQNFSATP NVTTCPMDEK LLSTVLTTSY SVIFIVGLVG NIIALYVFL GIHRKRNSIQ IYLLNVAIAD LLLIFCLPFR IMYHINQNKW TLGVILCKVV GTLFYMNMYI SIILLGFISL D RYIKINRS IQQRKAITTK QSIYVCCIVW MLALGGFLTM IILTLKKGGH NSTMCFHYRD KHNAKGEAIF NFILVVMFWL IF LLIILSY IKIGKNLLRI SKRRSKFPNS GKYATTARNS FIVLIIFTIC FVPYHAFRFI YISSQLNVSS CYWKEIVHKT NEI MLVLSS FNSCLDPVMY FLMSSNIRKI MCQLLFRRFQ GEPSRSESTS EFKPGYSLHD TSVAVKIQSS SKSTENLYFQ

UniProtKB: Probable G-protein coupled receptor 34

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Macromolecule #2: (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[(~{Z})-octadec-9-enoyl]o...

MacromoleculeName: (2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[(~{Z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: KW0
Molecular weightTheoretical: 551.65 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

Concentration12 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7dh5

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79925
FSC plot (resolution estimation)

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