9asb

Structure of human calcium-sensing receptor in complex with chimeric Gq (miniGisq) protein in nanodiscs

Method: ELECTRON MICROSCOPY Dmax: 215.4 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 Insufficient information 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 Chimeric mini guanine nucleotide-binding protein G(i)(s)(q) subunit alpha × 1 (P63096,A0A590UJY2) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Chimeric mini guanine nucleotide-binding protein G(i)(s)(q) subunit alpha × 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 × 6 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 3.40 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

Chimeric mini guanine nucleotide-binding protein G(i)(s)(q) subunit alpha

Homo sapiens

UniProt A0A590UJY2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 其他Polymer 4 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 50–237 Not recorded Isoform 1 of Extracellular calcium-sensing receptor × 2 (P41180) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Chimeric mini guanine nucleotide-binding protein G(i)(s)(q) subunit alpha × 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 × 6 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 3.40 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.

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A590UJY2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 69–246; UniProt 50–237

Chimeric mini guanine nucleotide-binding protein G(i)(s)(q) subunit alpha

Homo sapiens

UniProt P63096

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 其他Polymer 4 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–53 Not recorded Isoform 1 of Extracellular calcium-sensing receptor × 2 (P41180) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Chimeric mini guanine nucleotide-binding protein G(i)(s)(q) subunit alpha × 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 × 6 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 3.40 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.

573 other PDB entries and 591 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–53; UniProt 1–53

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 Insufficient information 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) Chimeric mini guanine nucleotide-binding protein G(i)(s)(q) subunit alpha × 1 (P63096,A0A590UJY2) Chimeric mini guanine nucleotide-binding protein G(i)(s)(q) subunit alpha × 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 × 6 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 3.40 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 10–348; UniProt 2–340

Chimeric mini guanine nucleotide-binding protein G(i)(s)(q) subunit alpha

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 Insufficient information 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) Chimeric mini guanine nucleotide-binding protein G(i)(s)(q) subunit alpha × 1 (P63096,A0A590UJY2) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) 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 × 6 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 3.40 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 9asb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9asb
Deposition date deposition_date2024-02-24
Structure title titleStructure of human calcium-sensing receptor in complex with chimeric Gq (miniGisq) 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_guinier74.29
Radius of gyration Rg (electron density) rg_electron74.36
Forward intensity I(0) i0887368000.00
Molecular weight molecular_weight258320.0 kDa
Excluded volume excluded_volume325660 ų
Envelope volume envelope_volume519360 ų
Hydration-shell volume shell_volume62327 ų
Envelope diameter envelope_diameter236.5
Shell Rg shell_rg61.66
Envelope Rg envelope_rg72.45
Shape Rg shape_rg74.33
Total Rg total_rg74.23
Total atoms total_atoms18185
Residues n_residues2241
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 dmax215.4
Rg (real space) rg_real74.95
Rg uncertainty (real space) rg_real_error1.96
I(0) (real space) i0_real8.8690e+08
I(0) uncertainty (real space) i0_real_error1.7030e+07
Rg (reciprocal space) rg_reciprocal71.08
I(0) (reciprocal space) i0_reciprocal880100000.0000
Solution quality estimate total_estimate0.6431
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary41.0
Skewness Skewness skewness0.368
Kurtosis Kurtosis kurtosis-1.092
Angular range angular_range— – 0.1050 −1
Current regularization parameter α current_alpha0.0011
Highest regularization parameter α highest_alpha21310000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.356; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.290; 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)