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- EMDB-63201: Cryo-EM structure of D1R in complex with de novo designed negativ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63201
TitleCryo-EM structure of D1R in complex with de novo designed negative allosteric GEM targeting TM5/6/7
Map data
Sample
  • Complex: mGlu2-mGlu4 heterodimer bound Gi
    • Protein or peptide: D(1A) dopamine receptor,Soluble cytochrome b562
    • Protein or peptide: De novo designed negative allosteric GPCR exoframe modulator targeting TM5/6/7
  • Ligand: CHOLESTEROL
  • Ligand: Flupentixol
  • Ligand: PALMITIC ACID
KeywordsGPCR / GEM / GPCR exoframe modulator / D1R / MEMBRANE PROTEIN
Function / homology
Function and homology information


dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / dopamine binding / operant conditioning / phospholipase C-activating dopamine receptor signaling pathway / peristalsis / heterotrimeric G-protein binding ...dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / dopamine binding / operant conditioning / phospholipase C-activating dopamine receptor signaling pathway / peristalsis / heterotrimeric G-protein binding / modification of postsynaptic structure / G protein-coupled receptor complex / positive regulation of neuron migration / habituation / grooming behavior / regulation of dopamine metabolic process / dopamine transport / astrocyte development / dentate gyrus development / sensitization / striatum development / positive regulation of potassium ion transport / conditioned taste aversion / maternal behavior / arrestin family protein binding / non-motile cilium / G protein-coupled dopamine receptor signaling pathway / long-term synaptic depression / adult walking behavior / mating behavior / : / ciliary membrane / temperature homeostasis / dopamine metabolic process / transmission of nerve impulse / G-protein alpha-subunit binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of synaptic transmission, glutamatergic / behavioral fear response / neuronal action potential / adenylate cyclase-activating adrenergic receptor signaling pathway / behavioral response to cocaine / synapse assembly / presynaptic modulation of chemical synaptic transmission / positive regulation of release of sequestered calcium ion into cytosol / response to amphetamine / synaptic transmission, glutamatergic / electron transport chain / visual learning / G protein-coupled receptor activity / vasodilation / GABA-ergic synapse / memory / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein import into nucleus / long-term synaptic potentiation / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / presynaptic membrane / G alpha (s) signalling events / dendritic spine / postsynaptic membrane / electron transfer activity / periplasmic space / positive regulation of MAPK cascade / cilium / positive regulation of cell migration / iron ion binding / response to xenobiotic stimulus / heme binding / endoplasmic reticulum membrane / glutamatergic synapse / nucleus / plasma membrane
Similarity search - Function
Dopamine D1 receptor / Dopamine receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Soluble cytochrome b562 / D(1A) dopamine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsGuo J / Zhou Y / Cheng S / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: GPCR exoframe modulator
Authors: Cheng S / Guo J / Zhou Y / Zhang Y
History
DepositionJan 17, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63201.png

Downloads & links

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Map

FileDownload / File: emd_63201.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 224 pix.
= 208.32 Å		0.93 Å/pix.
x 224 pix.
= 208.32 Å		0.93 Å/pix.
x 224 pix.
= 208.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00774
Minimum - Maximum-0.028323142 - 0.05287042
Average (Standard dev.)-0.0000041383896 (±0.001767408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 208.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63201_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_63201_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 : mGlu2-mGlu4 heterodimer bound Gi

EntireName: mGlu2-mGlu4 heterodimer bound Gi
Components
  • Complex: mGlu2-mGlu4 heterodimer bound Gi
    • Protein or peptide: D(1A) dopamine receptor,Soluble cytochrome b562
    • Protein or peptide: De novo designed negative allosteric GPCR exoframe modulator targeting TM5/6/7
  • Ligand: CHOLESTEROL
  • Ligand: Flupentixol
  • Ligand: PALMITIC ACID

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Supramolecule #1: mGlu2-mGlu4 heterodimer bound Gi

SupramoleculeName: mGlu2-mGlu4 heterodimer bound Gi / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: D(1A) dopamine receptor,Soluble cytochrome b562

MacromoleculeName: D(1A) dopamine receptor,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.093844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RTLNTSAMDG TGLVVERDFS VRILTACFLS LLILSTLLGN TLVCAAVIRF RHLRSKVTNF FVISLAVSDL LVAVLVMPWK AVAEIAGFW PFGSFCNIWV AFDIMCSTAS ILNLCVISVD RYWAISSPFR YERKMTPKAA FILISVAWTL SVLISFIPVQ L SWHKAKPT ...String:
RTLNTSAMDG TGLVVERDFS VRILTACFLS LLILSTLLGN TLVCAAVIRF RHLRSKVTNF FVISLAVSDL LVAVLVMPWK AVAEIAGFW PFGSFCNIWV AFDIMCSTAS ILNLCVISVD RYWAISSPFR YERKMTPKAA FILISVAWTL SVLISFIPVQ L SWHKAKPT SPSDGNATSL AETIDNCDSS LSRTYAISSS VISFYIPVAI MIVTYTRIYR ILKKELDALN DNWETLNDNL KV IEKADNA AQVKDALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKT TRDAIL KPFIEELKEL KGKPFLIDAV IMGVFVCCWL PFFILNCILP FCGSGETQPF CIDSNTFDVF VWFGWANSSL NPII YAFNA DFRKAFSTLL GCYRLCPATN NAIETVSINN NGAAMFSSHH EPRGSISKEC NLVYLIPHAV GSSEDLKKEE AAGIA RPLE KLSPALSVIL DYDTDVSLEK IQPITQNGQH PT

UniProtKB: D(1A) dopamine receptor, Soluble cytochrome b562, D(1A) dopamine receptor

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Macromolecule #2: De novo designed negative allosteric GPCR exoframe modulator targ...

MacromoleculeName: De novo designed negative allosteric GPCR exoframe modulator targeting TM5/6/7
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.962571 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PSPVPPPPPP LPIWKILLII GTILYIVVFL YISIFLYRLL KTFVPKEERK KWFKFLGILF LIFLILLIYF VVYVIRVLFP PPPPPSPGP PPPPPP

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: Flupentixol

MacromoleculeName: Flupentixol / type: ligand / ID: 4 / Number of copies: 1 / Formula: A1EKL
Molecular weightTheoretical: 434.518 Da

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Macromolecule #5: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 483651
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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