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- EMDB-36426: Structure of the adhesion GPCR ADGRL3 in the apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-36426
TitleStructure of the adhesion GPCR ADGRL3 in the apo state
Map data
Sample
  • Complex: ADGRL3-mBRIL complex
    • Protein or peptide: Adhesion G protein-coupled receptor L3,Soluble cytochrome b562
KeywordsADGRL3 / Apo form / MEMBRANE PROTEIN
Function / homology
Function and homology information


G protein-coupled receptor activity / electron transport chain / carbohydrate binding / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / iron ion binding / heme binding / membrane
Similarity search - Function
GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / Olfactomedin-like domain ...GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Adhesion G protein-coupled receptor L3 / Soluble cytochrome b562
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsTao Y / Guo Q / He B / Zhong Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2024
Title: A method for structure determination of GPCRs in various states.
Authors: Qiong Guo / Binbin He / Yixuan Zhong / Haizhan Jiao / Yinhang Ren / Qinggong Wang / Qiangqiang Ge / Yongxiang Gao / Xiangyu Liu / Yang Du / Hongli Hu / Yuyong Tao /
Abstract: G-protein-coupled receptors (GPCRs) are a class of integral membrane proteins that detect environmental cues and trigger cellular responses. Deciphering the functional states of GPCRs induced by ...G-protein-coupled receptors (GPCRs) are a class of integral membrane proteins that detect environmental cues and trigger cellular responses. Deciphering the functional states of GPCRs induced by various ligands has been one of the primary goals in the field. Here we developed an effective universal method for GPCR cryo-electron microscopy structure determination without the need to prepare GPCR-signaling protein complexes. Using this method, we successfully solved the structures of the β-adrenergic receptor (βAR) bound to antagonistic and agonistic ligands and the adhesion GPCR ADGRL3 in the apo state. For βAR, an intermediate state stabilized by the partial agonist was captured. For ADGRL3, the structure revealed that inactive ADGRL3 adopts a compact fold and that large unusual conformational changes on both the extracellular and intracellular sides are required for activation of adhesion GPCRs. We anticipate that this method will open a new avenue for understanding GPCR structure‒function relationships and drug development.
History
DepositionJun 5, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36426.png

Downloads & links

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Map

FileDownload / File: emd_36426.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.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-8.08412 - 9.515385
Average (Standard dev.)-0.00079709967 (±0.054434743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36426_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_36426_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : ADGRL3-mBRIL complex

EntireName: ADGRL3-mBRIL complex
Components
  • Complex: ADGRL3-mBRIL complex
    • Protein or peptide: Adhesion G protein-coupled receptor L3,Soluble cytochrome b562

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Supramolecule #1: ADGRL3-mBRIL complex

SupramoleculeName: ADGRL3-mBRIL complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Adhesion G protein-coupled receptor L3,Soluble cytochrome b562

MacromoleculeName: Adhesion G protein-coupled receptor L3,Soluble cytochrome b562
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.439922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKAV EAREIMWFKT RQGQIAKQPC PAGTIGVSTY LCLAPDGIWD PQGPDLSNCS SPWVNHITQK LKSGETAANI ARELAEQTR NHLNAGDITY SVRAMDQLVG LLDVQLRNLT PGGKDSAARS LNKLQKRERS CRAYVQAMVE TVNNLLQPQA L NAWRDLTT ...String:
DYKDDDDKAV EAREIMWFKT RQGQIAKQPC PAGTIGVSTY LCLAPDGIWD PQGPDLSNCS SPWVNHITQK LKSGETAANI ARELAEQTR NHLNAGDITY SVRAMDQLVG LLDVQLRNLT PGGKDSAARS LNKLQKRERS CRAYVQAMVE TVNNLLQPQA L NAWRDLTT SDQLRAATML LHTVEESAFV LADNLLKTDI VRENTDNIKL EVARLSTEGN LEDLKFPENM GHGSTIQLSA NT LKQNGRN GEIRVAFVLY NNLGPYLSTE NASMKLGTEA LSTNHSVIVN SPVITAAINK EFSNKVYLAD PVVFTVKHIK QSE ENFNPN CSFWSYSKRT MTGYWSTQGC RLLTTNKTHT TCSCNHLANF AVLMAHVEVK HSDAVHDLLL DVITWVGILL SLVC LLICI FTFCFFRGLQ SDRNTIHKNL CISLFVAELL FLIGINRTDQ PIACAVFAAL LHFFFLAAFT WMFLEGVQLY IMLVE VFES EHSRRKYFYL VGYGMPALIV AVSAAVDYRS YGTDKVCWLR LDTYFIWSFI GPATLIIMLN VIFLGIALYK MFHHTA DLE DNWETLNDNL KVIEKADNAA QVKDALTKMR AAALDAQKAS GSGSPEMKDF RHGFDILVGQ IDDALKLANE GKVKEAQ AA AEQLKTTRNA YIQKYLERAD NIKSWVIGAI ALLCLLGLTW AFGLMYINES TVIMAYLFTI FNSLQGMFIF IFHCVLQK K VRKEYGKCLR THAASRLEEE LRRRLTEGSH HHHHHHH

UniProtKB: Adhesion G protein-coupled receptor L3, Soluble cytochrome b562, Soluble cytochrome b562, Adhesion G protein-coupled receptor L3

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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: 7.4
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.0 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: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 706010
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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