7f23

Cryo-EM structure of the GTP-bound dopamine receptor 1 and mini-Gs complex with Nb35

Method: ELECTRON MICROSCOPY Dmax: 111.2 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 F; UniProt 1–446 Not recorded ;Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short ; × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Nanobody 35 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) LDP L-DOPAMINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.58 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 F; PDBConstruct 28–473; UniProt 1–446

;Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short ;

Homo sapiens

UniProt P63092

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 A; UniProt 6–64 Chain A; UniProt 190–380 Mutation:G49D, E50N, A235D, S238D, I358A, V361I D(1A) dopamine receptor × 1 (P21728) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Nanobody 35 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) LDP L-DOPAMINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.58 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.

348 other PDB entries and 356 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAS2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–59; UniProt 6–64 Author chain A; PDBConstruct 68–248; UniProt 190–380

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

Homo sapiens

UniProt P62873

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) ;Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short ; × 1 (P63092) Nanobody 35 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) LDP L-DOPAMINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.58 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.

1260 other PDB entries and 1263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 20–358; UniProt 2–340

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

Homo sapiens

UniProt P59768

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 D; UniProt 1–71 Mutation:C68S D(1A) dopamine receptor × 1 (P21728) ;Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short ; × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Nanobody 35 × 1 LDP L-DOPAMINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.58 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.

1233 other PDB entries and 1236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain D; PDBConstruct 1–71; UniProt 1–71

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 7f23

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7f23
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7f23
Deposition date deposition_date2021-06-10
Structure title titleCryo-EM structure of the GTP-bound dopamine receptor 1 and mini-Gs complex with Nb35
Keywords keywordsGPCR, dopamine receptor, mini-Gs, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.66
Radius of gyration Rg (electron density) rg_electron33.53
Forward intensity I(0) i0213592000.00
Molecular weight molecular_weight116530.0 kDa
Excluded volume excluded_volume145530 ų
Envelope volume envelope_volume184060 ų
Hydration-shell volume shell_volume46020 ų
Envelope diameter envelope_diameter118.2
Shell Rg shell_rg39.87
Envelope Rg envelope_rg33.56
Shape Rg shape_rg33.52
Total Rg total_rg34.03
Total atoms total_atoms8187
Residues n_residues1037
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 dmax111.2
Rg (real space) rg_real33.69
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real2.1360e+08
I(0) uncertainty (real space) i0_real_error3.2000e+06
Rg (reciprocal space) rg_reciprocal33.67
I(0) (reciprocal space) i0_reciprocal213600000.0000
Solution quality estimate total_estimate0.8811
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.9
Skewness Skewness skewness0.399
Kurtosis Kurtosis kurtosis-0.231
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45640000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.854

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7f23A01
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_id7f23B01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

8. Citations (1)

9. Files and Curves (10)