8ha0

Molecular recognition of two endogenous hormones by the human parathyroid hormone receptor-1

Method: ELECTRON MICROSCOPY Dmax: 157.8 Å Quality: REASONABLE

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

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 Guanine nucleotide-binding protein g(s) subunit alpha × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Nanobody 35 × 1 Parathyroid hormone × 1 (P01270) Parathyroid hormone/parathyroid hormone-related peptide receptor × 1 (Q03431) CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.62 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 2
Chains and sequence ranges Author chain B; PDBConstruct 36–374; 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 Guanine nucleotide-binding protein g(s) subunit alpha × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P54311) Nanobody 35 × 1 Parathyroid hormone × 1 (P01270) Parathyroid hormone/parathyroid hormone-related peptide receptor × 1 (Q03431) CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.62 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 3
Chains and sequence ranges Author chain G; PDBConstruct 1–71; UniProt 1–71

Parathyroid hormone

Homo sapiens

UniProt P01270

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 P; UniProt 32–65 Not recorded Guanine nucleotide-binding protein g(s) subunit alpha × 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 Parathyroid hormone/parathyroid hormone-related peptide receptor × 1 (Q03431) CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.62 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.

25 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTHY_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain P; PDBConstruct 1–34; UniProt 32–65

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 Not recorded Guanine nucleotide-binding protein g(s) subunit alpha × 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 Parathyroid hormone × 1 (P01270) CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.62 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.

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 6
Chains and sequence ranges Author chain R; PDBConstruct 1–476; UniProt 27–502

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 8ha0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ha0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ha0
Deposition date deposition_date2022-10-26
Structure title titleMolecular recognition of two endogenous hormones by the human parathyroid hormone receptor-1
Keywords keywordsPTH1R, GPCR, LIPID BINDING PROTEIN-HORMONE-IMMUNE SYSTEM complex; LIPID BINDING PROTEIN/HORMONE/IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier41.93
Radius of gyration Rg (electron density) rg_electron42.17
Forward intensity I(0) i0259368000.00
Molecular weight molecular_weight133350.0 kDa
Excluded volume excluded_volume167900 ų
Envelope volume envelope_volume223560 ų
Hydration-shell volume shell_volume48334 ų
Envelope diameter envelope_diameter166.2
Shell Rg shell_rg42.97
Envelope Rg envelope_rg42.76
Shape Rg shape_rg42.16
Total Rg total_rg42.23
Total atoms total_atoms9385
Residues n_residues1155
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 dmax157.8
Rg (real space) rg_real42.72
Rg uncertainty (real space) rg_real_error1.96
I(0) (real space) i0_real2.5940e+08
I(0) uncertainty (real space) i0_real_error5.2910e+06
Rg (reciprocal space) rg_reciprocal41.93
I(0) (reciprocal space) i0_reciprocal259100000.0000
Solution quality estimate total_estimate0.7237
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.4
Skewness Skewness skewness0.861
Kurtosis Kurtosis kurtosis0.267
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37360000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.375; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.597; Smooth: 0.682

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id8ha0B01
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_id8ha0N01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)