9avl

Structure of human calcium-sensing receptor in complex with Gi3 protein in nanodiscs

Method: ELECTRON MICROSCOPY Dmax: 217.7 Å Quality: REASONABLE

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

Isoform 1 of Extracellular calcium-sensing receptor

Homo sapiens

UniProt P41180

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 4 PDB declaration: pentameric(5) Consistent with protein copy count Chain Q; UniProt 1–903 Chain R; UniProt 1–903 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-3 × 1 (P08754) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 × 1 (P62879) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 TCR CYCLOMETHYLTRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 6 9IG 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1 A1AF7 (19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE;The sample was blotted for 6s before plunge-frozen. Resolution 3.80 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.

27 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CASR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain Q; PDBConstruct 1–911; UniProt 1–903 Author chain R; PDBConstruct 1–911; UniProt 1–903

Guanine nucleotide-binding protein G(i) subunit alpha-3

Homo sapiens

UniProt P08754

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 4 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–354 Mutation:S47N, G203A, E245A, A326S Isoform 1 of Extracellular calcium-sensing receptor × 2 (P41180) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 × 1 (P62879) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 TCR CYCLOMETHYLTRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 6 9IG 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1 A1AF7 (19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE;The sample was blotted for 6s before plunge-frozen. Resolution 3.80 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.

24 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–354; UniProt 1–354

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2

Homo sapiens

UniProt P62879

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 5 其他Polymer 4 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Isoform 1 of Extracellular calcium-sensing receptor × 2 (P41180) Guanine nucleotide-binding protein G(i) subunit alpha-3 × 1 (P08754) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 TCR CYCLOMETHYLTRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 6 9IG 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1 A1AF7 (19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE;The sample was blotted for 6s before plunge-frozen. Resolution 3.80 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name GBB2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain B; PDBConstruct 10–348; 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 Other combination Heteromer Protein × 5 其他Polymer 4 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Isoform 1 of Extracellular calcium-sensing receptor × 2 (P41180) Guanine nucleotide-binding protein G(i) subunit alpha-3 × 1 (P08754) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 × 1 (P62879) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 TCR CYCLOMETHYLTRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 6 9IG 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1 A1AF7 (19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE;The sample was blotted for 6s before plunge-frozen. Resolution 3.80 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 4
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 9avl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9avl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9avl
Deposition date deposition_date2024-03-04
Structure title titleStructure of human calcium-sensing receptor in complex with Gi3 protein in nanodiscs
Keywords keywordsCalcium-sensing receptor, G-protein-coupled receptor, G protein, signal transduction, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier75.73
Radius of gyration Rg (electron density) rg_electron75.89
Forward intensity I(0) i0881485000.00
Molecular weight molecular_weight257860.0 kDa
Excluded volume excluded_volume325240 ų
Envelope volume envelope_volume534270 ų
Hydration-shell volume shell_volume62987 ų
Envelope diameter envelope_diameter243.9
Shell Rg shell_rg61.44
Envelope Rg envelope_rg74.15
Shape Rg shape_rg75.85
Total Rg total_rg75.76
Total atoms total_atoms18143
Residues n_residues2245
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 dmax217.7
Rg (real space) rg_real76.40
Rg uncertainty (real space) rg_real_error1.72
I(0) (real space) i0_real8.8070e+08
I(0) uncertainty (real space) i0_real_error2.0870e+07
Rg (reciprocal space) rg_reciprocal72.20
I(0) (reciprocal space) i0_reciprocal873400000.0000
Solution quality estimate total_estimate0.6366
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary41.5
Skewness Skewness skewness0.371
Kurtosis Kurtosis kurtosis-1.098
Angular range angular_range— – 0.1050 −1
Current regularization parameter α current_alpha0.0017
Highest regularization parameter α highest_alpha24640000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.334; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.274; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (12)

8. Citations (1)

9. Files and Curves (10)