7ljc

Allosteric modulator LY3154207 binding to SKF-81297-bound dopamine receptor 1 in complex with miniGs protein

Method: ELECTRON MICROSCOPY Dmax: 113.8 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

D(1A) dopamine receptor

Homo sapiens

UniProt P21728

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 1–446 Not recorded Engineered human Gs alpha subunit × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Nanoboy 35 × 1 SK0 (1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol × 1 G4C 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone × 1 CLR CHOLESTEROL × 6 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

29 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DRD1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 49–494; UniProt 1–446

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Rattus norvegicus

UniProt P54311

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded D(1A) dopamine receptor × 1 (P21728) Engineered human Gs alpha subunit × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Nanoboy 35 × 1 SK0 (1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol × 1 G4C 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone × 1 CLR CHOLESTEROL × 6 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

161 other PDB entries and 162 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_RAT
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 15–353; UniProt 2–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Bos taurus

UniProt P63212

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 2–68 Not recorded D(1A) dopamine receptor × 1 (P21728) Engineered human Gs alpha subunit × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Nanoboy 35 × 1 SK0 (1R)-6-chloro-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine-7,8-diol × 1 G4C 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone × 1 CLR CHOLESTEROL × 6 PLM PALMITIC ACID × 6 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.2 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

215 other PDB entries and 216 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_BOVIN
Isoform
PDB entities 4
Chains and sequence ranges Author chain G; PDBConstruct 1–67; UniProt 2–68

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7ljc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ljc
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id7ljc
Deposition date deposition_date2021-01-28
Structure title titleAllosteric modulator LY3154207 binding to SKF-81297-bound dopamine receptor 1 in complex with miniGs protein
Keywords keywordsDopamine receptor 2, Gs protein, SKF-81297, PAM, LY3154207, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.35
Radius of gyration Rg (electron density) rg_electron33.93
Forward intensity I(0) i0212251000.00
Molecular weight molecular_weight121550.0 kDa
Excluded volume excluded_volume154070 ų
Envelope volume envelope_volume194810 ų
Hydration-shell volume shell_volume47630 ų
Envelope diameter envelope_diameter122.0
Shell Rg shell_rg40.52
Envelope Rg envelope_rg34.27
Shape Rg shape_rg33.90
Total Rg total_rg34.54
Total atoms total_atoms8544
Residues n_residues1040
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax113.8
Rg (real space) rg_real33.38
Rg uncertainty (real space) rg_real_error0.87
I(0) (real space) i0_real2.1230e+08
I(0) uncertainty (real space) i0_real_error3.7790e+06
Rg (reciprocal space) rg_reciprocal33.36
I(0) (reciprocal space) i0_reciprocal212200000.0000
Solution quality estimate total_estimate0.8716
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.7
Skewness Skewness skewness0.414
Kurtosis Kurtosis kurtosis-0.199
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha59570000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.912

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd7ljcb_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.4 — WD40 repeat-like
Family Family familyb.69.4.1 — WD40-repeat
Domain ID domain_idd7ljcg_
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.3 — Transducin (heterotrimeric G protein), gamma chain
Family Family familya.137.3.1 — Transducin (heterotrimeric G protein), gamma chain
Domain ID domain_idd7ljcn1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd7ljcn2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id7ljcA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id7ljcB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id7ljcN01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (2)

9. Files and Curves (10)