8szi

Cryo-EM structure of PAM-free human calcium-sensing receptor CaSR-Gi complex in lipid nanodiscs

Method: ELECTRON MICROSCOPY Dmax: 218.8 Å Quality: REASONABLE

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

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 3 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 1–354 Mutation:S47N, G203A, E245A, A326S Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Extracellular calcium-sensing receptor × 1 (P41180) Extracellular calcium-sensing receptor × 1 (P41180) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4 TRP TRYPTOPHAN × 3 PO4 PHOSPHATE ION × 2 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 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.

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 1
Chains and sequence ranges Author chain C; PDBConstruct 1–354; UniProt 1–354

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 Other combination Heteromer Protein × 5 其他Polymer 3 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 2–340 Not recorded 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) Extracellular calcium-sensing receptor × 1 (P41180) Extracellular calcium-sensing receptor × 1 (P41180) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4 TRP TRYPTOPHAN × 3 PO4 PHOSPHATE ION × 2 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 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.

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 2
Chains and sequence ranges Author chain D; PDBConstruct 5–343; 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 3 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 1–71 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-1 × 1 (P62873) Extracellular calcium-sensing receptor × 1 (P41180) Extracellular calcium-sensing receptor × 1 (P41180) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4 TRP TRYPTOPHAN × 3 PO4 PHOSPHATE ION × 2 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 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.

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 3
Chains and sequence ranges Author chain E; PDBConstruct 1–71; UniProt 1–71

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 3 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 19–894 Chain B; UniProt 19–894 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-1 × 1 (P62873) 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 × 3 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4 TRP TRYPTOPHAN × 3 PO4 PHOSPHATE ION × 2 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 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.

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 4, 5
Chains and sequence ranges Author chain A; PDBConstruct 11–886; UniProt 19–894 Author chain B; PDBConstruct 33–908; UniProt 19–894

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 8szi

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8szi
Deposition date deposition_date2023-05-29
Structure title titleCryo-EM structure of PAM-free human calcium-sensing receptor CaSR-Gi complex in lipid nanodiscs
Keywords keywords;Family C GPCR, Calcium-sensing Receptor (CaSR), Heterotrimeric G protein, Cryo-EM, Lipid Nanodiscs, Positive Allosteric Modulator, Membrane Protein, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier76.74
Radius of gyration Rg (electron density) rg_electron76.96
Forward intensity I(0) i0845806000.00
Molecular weight molecular_weight253560.0 kDa
Excluded volume excluded_volume320200 ų
Envelope volume envelope_volume546160 ų
Hydration-shell volume shell_volume63196 ų
Envelope diameter envelope_diameter243.3
Shell Rg shell_rg62.23
Envelope Rg envelope_rg75.38
Shape Rg shape_rg76.93
Total Rg total_rg76.80
Total atoms total_atoms17854
Residues n_residues2246
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 dmax218.8
Rg (real space) rg_real77.33
Rg uncertainty (real space) rg_real_error1.51
I(0) (real space) i0_real8.4460e+08
I(0) uncertainty (real space) i0_real_error1.7470e+07
Rg (reciprocal space) rg_reciprocal73.06
I(0) (reciprocal space) i0_reciprocal837700000.0000
Solution quality estimate total_estimate0.6453
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary43.8
Skewness Skewness skewness0.366
Kurtosis Kurtosis kurtosis-1.104
Angular range angular_range— – 0.1000 −1
Current regularization parameter α current_alpha0.0060
Highest regularization parameter α highest_alpha22080000.0000
Real-space data points n_real_points21
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.372; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.280; 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)