8dcs

Cryo-EM structure of cyanopindolol-bound beta1-adrenergic receptor in complex with heterotrimeric Gs-protein

Method: ELECTRON MICROSCOPY Dmax: 121.0 Å Quality: GOOD

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

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

Bos taurus

UniProt P62871

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 Nanobody 35 × 1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04896) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Endolysin,Endolysin,Beta-1 adrenergic receptor chimera × 1 (P00720) P32 Cyanopindolol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.50 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.

72 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 1–339; UniProt 2–340

Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

Bos taurus

UniProt P04896

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 1–380 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Nanobody 35 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Endolysin,Endolysin,Beta-1 adrenergic receptor chimera × 1 (P00720) P32 Cyanopindolol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.50 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.

41 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAS2_BOVIN
Isoform P04896-2
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 5–384; UniProt 1–380

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 1–71 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Nanobody 35 × 1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04896) Endolysin,Endolysin,Beta-1 adrenergic receptor chimera × 1 (P00720) P32 Cyanopindolol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.50 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 1–71; UniProt 1–71

Endolysin,Endolysin,Beta-1 adrenergic receptor chimera

Meleagris gallopavo

UniProt P00720

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 2–161 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Nanobody 35 × 1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P04896) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) P32 Cyanopindolol × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.50 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.

721 other PDB entries and 846 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENLYS_BPT4
Isoform
PDB entities 5
Chains and sequence ranges Author chain R; PDBConstruct 33–192; UniProt 2–161

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 8dcs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8dcs
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8dcs
Deposition date deposition_date2022-06-17
Structure title titleCryo-EM structure of cyanopindolol-bound beta1-adrenergic receptor in complex with heterotrimeric Gs-protein
Keywords keywordsbeta1-adrenergic receptor, cyanopindolol, partial agonist, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier34.43
Radius of gyration Rg (electron density) rg_electron34.45
Forward intensity I(0) i0195820000.00
Molecular weight molecular_weight112380.0 kDa
Excluded volume excluded_volume140740 ų
Envelope volume envelope_volume182460 ų
Hydration-shell volume shell_volume45014 ų
Envelope diameter envelope_diameter131.7
Shell Rg shell_rg39.99
Envelope Rg envelope_rg34.67
Shape Rg shape_rg34.46
Total Rg total_rg34.86
Total atoms total_atoms15707
Residues n_residues1000
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 dmax121.0
Rg (real space) rg_real34.56
Rg uncertainty (real space) rg_real_error1.24
I(0) (real space) i0_real1.9580e+08
I(0) uncertainty (real space) i0_real_error3.5700e+06
Rg (reciprocal space) rg_reciprocal34.48
I(0) (reciprocal space) i0_reciprocal195800000.0000
Solution quality estimate total_estimate0.8578
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.8
Skewness Skewness skewness0.508
Kurtosis Kurtosis kurtosis-0.081
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43350000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.911

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id8dcsB01
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_id8dcsN01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)