8hj5

Cryo-EM structure of Gq-coupled MRGPRX1 bound with Compound-16

Method: ELECTRON MICROSCOPY Dmax: 124.4 Å Quality: EXCELLENT

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

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Guanine nucleotide-binding protein G(q) subunit alpha × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv16 × 1 Soluble cytochrome b562,Mas-related G-protein coupled receptor member X1,LgBit × 1 (P0ABE7,Q96LB2) Nb35 × 1 U2U N-{2-[(1-aminoisoquinolin-6-yl)oxy]-4-methylphenyl}-2-methoxybenzene-1-sulfonamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(q) subunit alpha × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) scFv16 × 1 Soluble cytochrome b562,Mas-related G-protein coupled receptor member X1,LgBit × 1 (P0ABE7,Q96LB2) Nb35 × 1 U2U N-{2-[(1-aminoisoquinolin-6-yl)oxy]-4-methylphenyl}-2-methoxybenzene-1-sulfonamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 D; PDBConstruct 1–71; UniProt 1–71

Soluble cytochrome b562,Mas-related G-protein coupled receptor member X1,LgBit

Homo sapiens

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain F; UniProt 24–128 Mutation:M29W,H124I,R128L Guanine nucleotide-binding protein G(q) subunit alpha × 1 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) scFv16 × 1 Nb35 × 1 U2U N-{2-[(1-aminoisoquinolin-6-yl)oxy]-4-methylphenyl}-2-methoxybenzene-1-sulfonamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 5
Chains and sequence ranges Author chain F; PDBConstruct 36–140; UniProt 24–128

Soluble cytochrome b562,Mas-related G-protein coupled receptor member X1,LgBit

Homo sapiens

UniProt Q96LB2

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain F; UniProt 1–322 Mutation:M29W,H124I,R128L Guanine nucleotide-binding protein G(q) subunit alpha × 1 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) scFv16 × 1 Nb35 × 1 U2U N-{2-[(1-aminoisoquinolin-6-yl)oxy]-4-methylphenyl}-2-methoxybenzene-1-sulfonamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MRGX1_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain F; PDBConstruct 141–462; UniProt 1–322

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 8hj5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8hj5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8hj5
Deposition date deposition_date2022-11-22
Structure title titleCryo-EM structure of Gq-coupled MRGPRX1 bound with Compound-16
Keywords keywordsGPCR, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier37.99
Radius of gyration Rg (electron density) rg_electron37.96
Forward intensity I(0) i0285553000.00
Molecular weight molecular_weight137700.0 kDa
Excluded volume excluded_volume172590 ų
Envelope volume envelope_volume231420 ų
Hydration-shell volume shell_volume51699 ų
Envelope diameter envelope_diameter126.6
Shell Rg shell_rg42.85
Envelope Rg envelope_rg37.93
Shape Rg shape_rg37.96
Total Rg total_rg38.28
Total atoms total_atoms9678
Residues n_residues1232
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 dmax124.4
Rg (real space) rg_real37.95
Rg uncertainty (real space) rg_real_error1.01
I(0) (real space) i0_real2.8560e+08
I(0) uncertainty (real space) i0_real_error4.6910e+06
Rg (reciprocal space) rg_reciprocal37.98
I(0) (reciprocal space) i0_reciprocal285600000.0000
Solution quality estimate total_estimate0.9014
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.4
Skewness Skewness skewness0.236
Kurtosis Kurtosis kurtosis-0.581
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha53570000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.942

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id8hj5B01
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_id8hj5C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id8hj5C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)