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- EMDB-30472: Cryo-EM structure of human GABA(B) receptor bound to the antagoni... -

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Basic information

Entry
Database: EMDB / ID: EMD-30472
TitleCryo-EM structure of human GABA(B) receptor bound to the antagonist CGP54626
Map data
Sample
  • Complex: Gamma-aminobutyric acid type B receptor
    • Protein or peptide: Gamma-aminobutyric acid type B receptor subunit 1
    • Protein or peptide: Gamma-aminobutyric acid type B receptor subunit 2
  • Ligand: (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid
  • Ligand: UNKNOWN LIGAND
  • Ligand: CHOLESTEROL
KeywordsGPCR / GABA / Neurosignalling / Signaling protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / GABA B receptor activation / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / G protein-coupled GABA receptor complex / negative regulation of gamma-aminobutyric acid secretion / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / negative regulation of epinephrine secretion / negative regulation of dopamine secretion ...G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / GABA B receptor activation / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / G protein-coupled GABA receptor complex / negative regulation of gamma-aminobutyric acid secretion / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / negative regulation of epinephrine secretion / negative regulation of dopamine secretion / positive regulation of growth hormone secretion / extracellular matrix protein binding / GABA receptor complex / negative regulation of adenylate cyclase activity / positive regulation of glutamate secretion / Class C/3 (Metabotropic glutamate/pheromone receptors) / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / negative regulation of synaptic transmission / axolemma / GABA-ergic synapse / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / dendritic shaft / response to nicotine / mitochondrial membrane / Schaffer collateral - CA1 synapse / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / osteoblast differentiation / transmembrane signaling receptor activity / synaptic vesicle / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / response to ethanol / dendritic spine / neuron projection / protein heterodimerization activity / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / endoplasmic reticulum membrane / extracellular space / plasma membrane / cytoplasm
Similarity search - Function
GPCR family 3, gamma-aminobutyric acid receptor, type B2 / Gamma-aminobutyric acid type B receptor subunit 2, coiled-coil domain / Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain / GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal ...GPCR family 3, gamma-aminobutyric acid receptor, type B2 / Gamma-aminobutyric acid type B receptor subunit 2, coiled-coil domain / Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain / GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Gamma-aminobutyric acid type B receptor subunit 2 / Gamma-aminobutyric acid type B receptor subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsKim Y / Jeong E
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Other privateSamsung Science and Technology Foundation SSTF-BA1602-14 Korea, Republic Of
CitationJournal: J Mol Biol / Year: 2020
Title: Structural Basis for Activation of the Heterodimeric GABA Receptor.
Authors: Yoojoong Kim / Eunyoung Jeong / Ji-Hong Jeong / Youngjin Kim / Yunje Cho /
Abstract: The neurotransmitter γ-aminobutyric acid (GABA) activates the metabotropic GABA receptor to generate slow, prolonged inhibitory signals that regulate the neural circuitry. The GABA receptor is an ...The neurotransmitter γ-aminobutyric acid (GABA) activates the metabotropic GABA receptor to generate slow, prolonged inhibitory signals that regulate the neural circuitry. The GABA receptor is an obligate heterodimeric G protein-coupled receptor (GPCR) comprised of GBR1 and GBR2 subunits, each with extracellular, seven-helix transmembrane (7TM), and coiled-coil domains. To understand how GABA-driven conformational changes in the extracellular domain are transmitted to the 7TM domain during signal transduction, we determined cryo-electron microscopy (EM) structures of GABA in two different states: an antagonist-bound inactive state, and an active state in which both the GABA agonist and a positive allosteric modulator (PAM) are bound. In the inactive state, the TM3 and TM5 helices in the two 7TM domains engage in cholesterol-mediated as well as direct interactions, resulting in an open conformation. GABA binding forces the extracellular domains of GBR1 and GBR2 into a compact form, relocating the linkers that connect the extracellular and 7TM domains closer to each other. The movement of the linker along with the associated extracellular loop 2 of the 7TM domain reorients the two 7TM domains and creates a new interface with the TM5, TM6 and TM7 helices in a closed conformation. PAM binding to the interface between the TM6 and TM6 helices stabilizes the active 7TM domain conformation. The relayed structural rearrangement results in significant conformational changes in the TM helices, as well as intracellular loop 3 in GBR2, which may promote the binding and activation of the Gi/o proteins.
History
DepositionAug 23, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cum
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30472.png

Downloads & links

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Map

FileDownload / File: emd_30472.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 230 pix.
= 250.7 Å		1.09 Å/pix.
x 230 pix.
= 250.7 Å		1.09 Å/pix.
x 230 pix.
= 250.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.05183517 - 0.0977024
Average (Standard dev.)-0.00000016048199 (±0.0031458195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 250.70001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z250.700250.700250.700
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-0.0520.098-0.000

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Supplemental data

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Sample components

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Entire : Gamma-aminobutyric acid type B receptor

EntireName: Gamma-aminobutyric acid type B receptor
Components
  • Complex: Gamma-aminobutyric acid type B receptor
    • Protein or peptide: Gamma-aminobutyric acid type B receptor subunit 1
    • Protein or peptide: Gamma-aminobutyric acid type B receptor subunit 2
  • Ligand: (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid
  • Ligand: UNKNOWN LIGAND
  • Ligand: CHOLESTEROL

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Supramolecule #1: Gamma-aminobutyric acid type B receptor

SupramoleculeName: Gamma-aminobutyric acid type B receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Antagonist-bound Gamma-aminobutyric acid type B receptor
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 kDa/nm

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Macromolecule #1: Gamma-aminobutyric acid type B receptor subunit 1

MacromoleculeName: Gamma-aminobutyric acid type B receptor subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.248195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRLLTALFAY FIVALILAFS VSAKSMSERR AVYIGALFPM SGGWPGGQAC QPAVEMALED VNSRRDILPD YELKLIHHDS KCDPGQATK YLYELLYNDP IKIILMPGCS SVSTLVAEAA RMWNLIVLSY GSSSPALSNR QRFPTFFRTH PSATLHNPTR V KLFEKWGW ...String:
MRLLTALFAY FIVALILAFS VSAKSMSERR AVYIGALFPM SGGWPGGQAC QPAVEMALED VNSRRDILPD YELKLIHHDS KCDPGQATK YLYELLYNDP IKIILMPGCS SVSTLVAEAA RMWNLIVLSY GSSSPALSNR QRFPTFFRTH PSATLHNPTR V KLFEKWGW KKIATIQQTT EVFTSTLDDL EERVKEAGIE ITFRQSFFSD PAVPVKNLKR QDARIIVGLF YETEARKVFC EV YKERLFG KKYVWFLIGW YADNWFKIYD PSINCTVDEM TEAVEGHITT EIVMLNPANT RSISNMTSQE FVEKLTKRLK RHP EETGGF QEAPLAYDAI WALALALNKT SGGGGRSGVR LEDFNYNNQT ITDQIYRAMN SSSFEGVSGH VVFDASGSRM AWTL IEQLQ GGSYKKIGYY DSTKDDLSWS KTDKWIGGSP PADQTLVIKT FRFLSQKLFI SVSVLSSLGI VLAVVCLSFN IYNSH VRYI QNSQPNLNNL TAVGCSLALA AVFPLGLDGY HIGRNQFPFV CQARLWLLGL GFSLGYGSMF TKIWWVHTVF TKKEEK KEW RKTLEPWKLY ATVGLLVGMD VLTLAIWQIV DPLHRTIETF AKEEPKEDID VSILPQLEHC SSRKMNTWLG IFYGYKG LL LLLGIFLAYE TKSVSTEKIN DHRAVGMAIY NVAVLCLITA PVTMILSSQQ DAAFAFASLA IVFSSYITLV VLFVPKMR R LITRGEWQSE AQDTMKTGSS TNNNEEEKSR LLEKENRELE KSGRLEVLFQ

UniProtKB: Gamma-aminobutyric acid type B receptor subunit 1

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Macromolecule #2: Gamma-aminobutyric acid type B receptor subunit 2

MacromoleculeName: Gamma-aminobutyric acid type B receptor subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.231258 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASPRSSGQP GPPPPPPPPP ARLLLLLLLP LLLPLAPGAW GWARGAPRPP PSSPPLSIMG LMPLTKEVAK GSIGRGVLPA VELAIEQIR NESLLRPYFL DLRLYDTECD NAKGLKAFYD AIKYGPNHLM VFGGVCPSVT SIIAESLQGW NLVQLSFAAT T PVLADKKK ...String:
MASPRSSGQP GPPPPPPPPP ARLLLLLLLP LLLPLAPGAW GWARGAPRPP PSSPPLSIMG LMPLTKEVAK GSIGRGVLPA VELAIEQIR NESLLRPYFL DLRLYDTECD NAKGLKAFYD AIKYGPNHLM VFGGVCPSVT SIIAESLQGW NLVQLSFAAT T PVLADKKK YPYFFRTVPS DNAVNPAILK LLKHYQWKRV GTLTQDVQRF SEVRNDLTGV LYGEDIEISD TESFSNDPCT SV KKLKGND VRIILGQFDQ NMAAKVFCCA YEENMYGSKY QWIIPGWYEP SWWEQVHTEA NSSRCLRKNL LAAMEGYIGV DFE PLSSKQ IKTISGKTPQ QYEREYNNKR SGVGPSKFHG YAYDGIWVIA KTLQRAMETL HASSRHQRIQ DFNYTDHTLG RIIL NAMNE TNFFGVTGQV VFRNGERMGT IKFTQFQDSR EVKVGEYNAV ADTLEIINDT IRFQGSEPPK DKTIILEQLR KISLP LYSI LSALTILGMI MASAFLFFNI KNRNQKLIKM SSPYMNNLII LGGMLSYASI FLFGLDGSFV SEKTFETLCT VRTWIL TVG YTTAFGAMFA KTWRVHAIFK NVKMKKKIIK DQKLLVIVGG MLLIDLCILI CWQAVDPLRR TVEKYSMEPD PAGRDIS IR PLLEHCENTH MTIWLGIVYA YKGLLMLFGC FLAWETRNVS IPALNDSKYI GMSVYNVGIM CIIGAAVSFL TRDQPNVQ F CIVALVIIFC STITLCLVFV PKLITLRTNP DAATQNRRFQ FTQNQKKEDS KTSTSVTSVN QASTSRSGRG GSENLYFQG GSGSGGDYKD DDDKDYKDDD DK

UniProtKB: Gamma-aminobutyric acid type B receptor subunit 2

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Macromolecule #3: (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]...

MacromoleculeName: (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid
type: ligand / ID: 3 / Number of copies: 1 / Formula: 2BV
Molecular weightTheoretical: 408.3 Da
Chemical component information

ChemComp-2BV:
(R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid

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Macromolecule #4: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 4 / Number of copies: 2 / Formula: UNL
Molecular weightTheoretical: 814.167 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 16 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 512675
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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