8hnl

CXCR3-DNGi complex activated by PS372424

Method: ELECTRON MICROSCOPY Dmax: 126.0 Å Quality: GOOD

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

Guanine nucleotide-binding protein G(i) subunit alpha-1

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 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–354 Not recorded 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) Soluble cytochrome b562,C-X-C chemokine receptor type 3,Oplophorus-luciferin 2-monooxygenase catalytic subunit × 1 (P0ABE7,P49682,Q9GV45) single-chain variable fragment scFv16 × 1 CLR CHOLESTEROL × 2 4AI (3S)-N-[(2S)-5-carbamimidamido-1-(cyclohexylmethylamino)-1-oxidanylidene-pentan-2-yl]-2-(4-oxidanylidene-4-phenyl-butanoyl)-3,4-dihydro-1H-isoquinoline-3-carboxamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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 1
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-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 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Soluble cytochrome b562,C-X-C chemokine receptor type 3,Oplophorus-luciferin 2-monooxygenase catalytic subunit × 1 (P0ABE7,P49682,Q9GV45) single-chain variable fragment scFv16 × 1 CLR CHOLESTEROL × 2 4AI (3S)-N-[(2S)-5-carbamimidamido-1-(cyclohexylmethylamino)-1-oxidanylidene-pentan-2-yl]-2-(4-oxidanylidene-4-phenyl-butanoyl)-3,4-dihydro-1H-isoquinoline-3-carboxamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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 B; PDBConstruct 23–361; 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 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Soluble cytochrome b562,C-X-C chemokine receptor type 3,Oplophorus-luciferin 2-monooxygenase catalytic subunit × 1 (P0ABE7,P49682,Q9GV45) single-chain variable fragment scFv16 × 1 CLR CHOLESTEROL × 2 4AI (3S)-N-[(2S)-5-carbamimidamido-1-(cyclohexylmethylamino)-1-oxidanylidene-pentan-2-yl]-2-(4-oxidanylidene-4-phenyl-butanoyl)-3,4-dihydro-1H-isoquinoline-3-carboxamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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 G; PDBConstruct 1–71; UniProt 1–71

Soluble cytochrome b562,C-X-C chemokine receptor type 3,Oplophorus-luciferin 2-monooxygenase catalytic subunit

Oplophorus gracilirostris

UniProt P0ABE7

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 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 23–127 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) 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) single-chain variable fragment scFv16 × 1 CLR CHOLESTEROL × 2 4AI (3S)-N-[(2S)-5-carbamimidamido-1-(cyclohexylmethylamino)-1-oxidanylidene-pentan-2-yl]-2-(4-oxidanylidene-4-phenyl-butanoyl)-3,4-dihydro-1H-isoquinoline-3-carboxamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 27–131; UniProt 23–127

Soluble cytochrome b562,C-X-C chemokine receptor type 3,Oplophorus-luciferin 2-monooxygenase catalytic subunit

Oplophorus gracilirostris

UniProt P49682

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 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 1–361 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) 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) single-chain variable fragment scFv16 × 1 CLR CHOLESTEROL × 2 4AI (3S)-N-[(2S)-5-carbamimidamido-1-(cyclohexylmethylamino)-1-oxidanylidene-pentan-2-yl]-2-(4-oxidanylidene-4-phenyl-butanoyl)-3,4-dihydro-1H-isoquinoline-3-carboxamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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.

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CXCR3_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 139–499; UniProt 1–361

Soluble cytochrome b562,C-X-C chemokine receptor type 3,Oplophorus-luciferin 2-monooxygenase catalytic subunit

Oplophorus gracilirostris

UniProt Q9GV45

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 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 27–184 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) 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) single-chain variable fragment scFv16 × 1 CLR CHOLESTEROL × 2 4AI (3S)-N-[(2S)-5-carbamimidamido-1-(cyclohexylmethylamino)-1-oxidanylidene-pentan-2-yl]-2-(4-oxidanylidene-4-phenyl-butanoyl)-3,4-dihydro-1H-isoquinoline-3-carboxamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 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.

21 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LUCI_OPLGR
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 500–657; UniProt 27–184

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 8hnl

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8hnl
Deposition date deposition_date2022-12-08
Structure title titleCXCR3-DNGi complex activated by PS372424
Keywords keywordsG protein coupled receptor, chemokine receptor, CXCR3, PS372424, 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_guinier38.15
Radius of gyration Rg (electron density) rg_electron37.88
Forward intensity I(0) i0240815000.00
Molecular weight molecular_weight127330.0 kDa
Excluded volume excluded_volume160130 ų
Envelope volume envelope_volume210130 ų
Hydration-shell volume shell_volume47731 ų
Envelope diameter envelope_diameter126.9
Shell Rg shell_rg42.12
Envelope Rg envelope_rg37.58
Shape Rg shape_rg37.86
Total Rg total_rg38.21
Total atoms total_atoms8944
Residues n_residues1135
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 dmax126.0
Rg (real space) rg_real38.12
Rg uncertainty (real space) rg_real_error0.97
I(0) (real space) i0_real2.4080e+08
I(0) uncertainty (real space) i0_real_error3.8670e+06
Rg (reciprocal space) rg_reciprocal38.14
I(0) (reciprocal space) i0_reciprocal240800000.0000
Solution quality estimate total_estimate0.8951
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.2
Skewness Skewness skewness0.225
Kurtosis Kurtosis kurtosis-0.584
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37120000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.898

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)