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- EMDB-60993: Cryo-EM structure of GPR55-Fab-Nb-ONO-9710531 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60993
TitleCryo-EM structure of GPR55-Fab-Nb-ONO-9710531 complex
Map data
Sample
  • Complex: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody
    • Protein or peptide: G-protein coupled receptor 55,Soluble cytochrome b562
    • Protein or peptide: anti-BRIL Fab Heavy chain
    • Protein or peptide: anti-BRIL Fab Light chain
    • Protein or peptide: anti-Fab Nanobody
  • Ligand: 4-(3-bromanyl-5-ethoxy-4-oxidanyl-phenyl)-~{N}-(2-methoxyphenyl)-2-methyl-5-oxidanylidene-4,6,7,8-tetrahydro-1~{H}-quinoline-3-carboxamide
KeywordsGPCR / G protein / cryo-EM / membrane protein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


cannabinoid receptor activity / Class A/1 (Rhodopsin-like receptors) / positive regulation of Rho protein signal transduction / negative regulation of osteoclast differentiation / bone resorption / electron transport chain / G protein-coupled receptor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade ...cannabinoid receptor activity / Class A/1 (Rhodopsin-like receptors) / positive regulation of Rho protein signal transduction / negative regulation of osteoclast differentiation / bone resorption / electron transport chain / G protein-coupled receptor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / electron transfer activity / periplasmic space / G protein-coupled receptor signaling pathway / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
Soluble cytochrome b562 / G-protein coupled receptor 55
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsHua T / Liu ZJ / Cherezov V / Chang H / Li XT / Shen L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91953202 China
CitationJournal: Cell Res / Year: 2025
Title: Structure basis of ligand recognition and activation of GPR55.
Authors: Hao Chang / Xiaoting Li / Ling Shen / Xuanrui Ge / Shuming Hao / Lijie Wu / Shenhui Liu / Junlin Liu / Vadim Cherezov / Tian Hua /
History
DepositionJul 30, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60993.png

Downloads & links

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Map

FileDownload / File: emd_60993.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.616 Å		0.83 Å/pix.
x 288 pix.
= 239.616 Å		0.83 Å/pix.
x 288 pix.
= 239.616 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.001793825 - 1.6755103
Average (Standard dev.)0.001111285 (±0.023839077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60993_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_60993_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody

EntireName: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody
Components
  • Complex: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody
    • Protein or peptide: G-protein coupled receptor 55,Soluble cytochrome b562
    • Protein or peptide: anti-BRIL Fab Heavy chain
    • Protein or peptide: anti-BRIL Fab Light chain
    • Protein or peptide: anti-Fab Nanobody
  • Ligand: 4-(3-bromanyl-5-ethoxy-4-oxidanyl-phenyl)-~{N}-(2-methoxyphenyl)-2-methyl-5-oxidanylidene-4,6,7,8-tetrahydro-1~{H}-quinoline-3-carboxamide

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Supramolecule #1: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody

SupramoleculeName: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 173 KDa

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Macromolecule #1: G-protein coupled receptor 55,Soluble cytochrome b562

MacromoleculeName: G-protein coupled receptor 55,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.058051 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SGDCLFDGVN ELMKTLQFAV HIPTFVLGLL LNLLAIHVFS TFLKNRWPDY AATSIYMINL AVFDLLLVLS LPFKMVLSQV QSPFPSLCT LVECLYFVSM YGSVWTICFI SMDRFLAIRY PLLVSHLRSP RKAFGICCTI WVLVWTGSIP IYSFHGKVEK Y MCFHNMSD ...String:
SGDCLFDGVN ELMKTLQFAV HIPTFVLGLL LNLLAIHVFS TFLKNRWPDY AATSIYMINL AVFDLLLVLS LPFKMVLSQV QSPFPSLCT LVECLYFVSM YGSVWTICFI SMDRFLAIRY PLLVSHLRSP RKAFGICCTI WVLVWTGSIP IYSFHGKVEK Y MCFHNMSD DTWSAKVFFP LEVFGFLLPM GIMGFCCSRS IHILLGRRDH TQDWVQQKAC IYTIAASLAV FVVSFLPVHL GF FLQFLVR NSFIVECRAK QSISFFLQLS MCFSNVNCCL DVFIYYFVIK EFRMNIRAHR PSADLEDNWE TLNDNLKVIE KAD NAAQVK DALTKMRAAA LDAQKATPPK LEDKSPDSPE MKDFRHGFDI LVGQIDDALK LANEGKVKEA QAAAEQLKTT RNAY IQKYL ERARSTL

UniProtKB: G-protein coupled receptor 55, Soluble cytochrome b562

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Macromolecule #2: anti-BRIL Fab Heavy chain

MacromoleculeName: anti-BRIL Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.152279 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: WSCIILFLVA TATGVHSEIS EVQLVESGGG LVQPGGSLRL SCAASGFNVR SFSIHWVRQA PGKGLEWVAY ISSSSGSTSY ADSVKGRFT ISADTSKNTA YLQMNSLRAE DTAVYYCARW GYWPGEPWWK AFDYWGQGTL VTVSSASTKG PSVFPLAPSS K STSGGTAA ...String:
WSCIILFLVA TATGVHSEIS EVQLVESGGG LVQPGGSLRL SCAASGFNVR SFSIHWVRQA PGKGLEWVAY ISSSSGSTSY ADSVKGRFT ISADTSKNTA YLQMNSLRAE DTAVYYCARW GYWPGEPWWK AFDYWGQGTL VTVSSASTKG PSVFPLAPSS K STSGGTAA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DK KVEPKS

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Macromolecule #3: anti-BRIL Fab Light chain

MacromoleculeName: anti-BRIL Fab Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.499129 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: anti-Fab Nanobody

MacromoleculeName: anti-Fab Nanobody / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.390644 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
GSQVQLQESG GGLVQPGGSL RLSCAASGRT ISRYAMSWFR QAPGKEREFV AVARRSGDGA FYADSVQGRF TVSRDDAKNT VYLQMNSLK PEDTAVYYCA IDSDTFYSGS YDYWGQGTQV TVSS

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Macromolecule #5: 4-(3-bromanyl-5-ethoxy-4-oxidanyl-phenyl)-~{N}-(2-methoxyphenyl)-...

MacromoleculeName: 4-(3-bromanyl-5-ethoxy-4-oxidanyl-phenyl)-~{N}-(2-methoxyphenyl)-2-methyl-5-oxidanylidene-4,6,7,8-tetrahydro-1~{H}-quinoline-3-carboxamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1L3E
Molecular weightTheoretical: 527.407 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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
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

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

6ww2


Details: GPR55:AlphaFOLD2 other:6WW2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 452996
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT / Overall B value: 145.1
Output model

PDB-9iya:
Cryo-EM structure of GPR55-Fab-Nb-ONO-9710531 complex

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