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- EMDB-63203: Cryo-EM structure of D1R in complex with de novo designed GEM tar... -

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Basic information

Entry
Database: EMDB / ID: EMD-63203
TitleCryo-EM structure of D1R in complex with de novo designed GEM targeting TM1/2/4 and GEM targeting TM3/4/5, and negative allosteric GEM targeting TM5/6/7
Map data
Sample
  • Complex: Complex of D1R with de novo designed GEM targetingTM1/2/4 and GEM targeting TM3/4/5, and negative allosteric GEM targeting TM5/6/7
    • Protein or peptide: D(1A) dopamine receptor
  • Protein or peptide: De novo designed GPCR exoframe modulator targeting TM1/2/4
  • Protein or peptide: De novo designed GPCR exoframe modulator targeting TM3/4/5
  • Protein or peptide: De novo designed negative allosteric GPCR exoframe modulator targeting TM5/6/7
  • Ligand: Flupentixol
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 / 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 / positive regulation of MAPK cascade / cilium / positive regulation of cell migration / response to xenobiotic stimulus / endoplasmic reticulum membrane / glutamatergic synapse / nucleus / plasma membrane
Similarity search - Function
Dopamine D1 receptor / Dopamine receptor family / 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
D(1A) dopamine receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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 modulators
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_63203.png

Downloads & links

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Map

FileDownload / File: emd_63203.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 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: 0.349
Minimum - Maximum-7.026846 - 7.89593
Average (Standard dev.)0.00059917226 (±0.05861397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63203_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_63203_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 : Complex of D1R with de novo designed GEM targetingTM1/2/4 and GEM...

EntireName: Complex of D1R with de novo designed GEM targetingTM1/2/4 and GEM targeting TM3/4/5, and negative allosteric GEM targeting TM5/6/7
Components
  • Complex: Complex of D1R with de novo designed GEM targetingTM1/2/4 and GEM targeting TM3/4/5, and negative allosteric GEM targeting TM5/6/7
    • Protein or peptide: D(1A) dopamine receptor
  • Protein or peptide: De novo designed GPCR exoframe modulator targeting TM1/2/4
  • Protein or peptide: De novo designed GPCR exoframe modulator targeting TM3/4/5
  • Protein or peptide: De novo designed negative allosteric GPCR exoframe modulator targeting TM5/6/7
  • Ligand: Flupentixol

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Supramolecule #1: Complex of D1R with de novo designed GEM targetingTM1/2/4 and GEM...

SupramoleculeName: Complex of D1R with de novo designed GEM targetingTM1/2/4 and GEM targeting TM3/4/5, and negative allosteric GEM targeting TM5/6/7
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: D(1A) dopamine receptor

MacromoleculeName: D(1A) dopamine receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.222922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RTLNTSAMDG TGLVVERDFS VRILTACFLS LLILSTLLGN TLVCAAVIRF RHLRSKVTNF FVISLAVSDL LVAVLVMPWK AVAEIAGFW PFGSFCNIWV AFDIMCSTAS ILNLCVISVD RYWAISSPFR YERKMTPKAA FILISVAWTL SVLISFIPVQ L SNHKAKPT ...String:
RTLNTSAMDG TGLVVERDFS VRILTACFLS LLILSTLLGN TLVCAAVIRF RHLRSKVTNF FVISLAVSDL LVAVLVMPWK AVAEIAGFW PFGSFCNIWV AFDIMCSTAS ILNLCVISVD RYWAISSPFR YERKMTPKAA FILISVAWTL SVLISFIPVQ L SNHKAKPT 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 PTGGS

UniProtKB: D(1A) dopamine receptor, D(1A) dopamine receptor

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Macromolecule #2: De novo designed GPCR exoframe modulator targeting TM1/2/4

MacromoleculeName: De novo designed GPCR exoframe modulator targeting TM1/2/4
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.438839 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
DYKDDDDKEF LEVLFQGPML LIIGTIITLV SSIIFLISFF RFMRKWIRGL TRRDVRRFLV VLLVFFLLFL ISLLLYVLFL VLYFLSLGK IDPKTGSA

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Macromolecule #3: De novo designed GPCR exoframe modulator targeting TM3/4/5

MacromoleculeName: De novo designed GPCR exoframe modulator targeting TM3/4/5
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.862196 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
GPPLPLSKIV ILLIILLILS IIFLLLLYLL IKYFKSFNEP IPPMLKVFLI YCVLSLIWVI IYTIIEVLEL LLRPPPG

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.962571 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
PSPVPPPPPP LPIWKILLII GTILYIVVFL YISIFLYRLL KTFVPKEERK KWFKFLGILF LIFLILLIYF VVYVIRVLFP PPPPPSPGP PPPPPP

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Macromolecule #5: Flupentixol

MacromoleculeName: Flupentixol / type: ligand / ID: 5 / Number of copies: 1 / Formula: A1EKL
Molecular weightTheoretical: 434.518 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
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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 314295
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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