6nbh

Cryo-EM structure of parathyroid hormone receptor type 1 in complex with a long-acting parathyroid hormone analog and G protein

Method: ELECTRON MICROSCOPY Dmax: 159.0 Å Quality: REASONABLE

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

Parathyroid hormone/parathyroid hormone-related peptide receptor

Homo sapiens

UniProt Q03431

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 27–502 Mutation:G188A Long-acting parathyroid hormone analog × 1 Gs protein 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) Nanobody-35 × 1 CLR CHOLESTEROL × 7 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 Å R-free 0.420

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.

43 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTH1R_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 1–476; UniProt 27–502

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Parathyroid hormone/parathyroid hormone-related peptide receptor × 1 (Q03431) Long-acting parathyroid hormone analog × 1 Gs protein alpha subunit × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Nanobody-35 × 1 CLR CHOLESTEROL × 7 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 Å R-free 0.420

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 4
Chains and sequence ranges Author chain B; PDBConstruct 7–345; 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Parathyroid hormone/parathyroid hormone-related peptide receptor × 1 (Q03431) Long-acting parathyroid hormone analog × 1 Gs protein alpha subunit × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Nanobody-35 × 1 CLR CHOLESTEROL × 7 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 Å R-free 0.420

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 5
Chains and sequence ranges Author chain G; 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 6nbh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6nbh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6nbh
Deposition date deposition_date2018-12-07
Structure title titleCryo-EM structure of parathyroid hormone receptor type 1 in complex with a long-acting parathyroid hormone analog and G protein
Keywords keywordsParathyroid hormone receptor, GPCR, Class B GPCR, GPCR-G protein complex, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier42.67
Radius of gyration Rg (electron density) rg_electron42.98
Forward intensity I(0) i0258400000.00
Molecular weight molecular_weight134920.0 kDa
Excluded volume excluded_volume170680 ų
Envelope volume envelope_volume239410 ų
Hydration-shell volume shell_volume50441 ų
Envelope diameter envelope_diameter168.4
Shell Rg shell_rg43.63
Envelope Rg envelope_rg44.09
Shape Rg shape_rg42.96
Total Rg total_rg43.08
Total atoms total_atoms9502
Residues n_residues1159
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 dmax159.0
Rg (real space) rg_real43.46
Rg uncertainty (real space) rg_real_error2.05
I(0) (real space) i0_real2.5840e+08
I(0) uncertainty (real space) i0_real_error5.3480e+06
Rg (reciprocal space) rg_reciprocal42.68
I(0) (reciprocal space) i0_reciprocal258200000.0000
Solution quality estimate total_estimate0.7192
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.7
Skewness Skewness skewness0.827
Kurtosis Kurtosis kurtosis0.158
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha45830000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.391; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.541; Smooth: 0.630

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id6nbhA00
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_id6nbhB00
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_id6nbhG00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily10 — Transducin (heterotrimeric G protein), gamma chain

8. Citations (1)

9. Files and Curves (10)