9d4z

CryoEM structure of PAR1 with endogenous tethered ligand

Method: ELECTRON MICROSCOPY Dmax: 118.5 Å Quality: GOOD

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 Protein heterocomplex 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)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Proteinase-activated receptor 1 × 1 (P25116) scFv16 × 1 Guanine nucleotide-binding protein G(q) subunit alpha chimera × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.74 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 1
Chains and sequence ranges Author chain B; PDBConstruct 1–339; 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 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 5–63 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Proteinase-activated receptor 1 × 1 (P25116) scFv16 × 1 Guanine nucleotide-binding protein G(q) subunit alpha chimera × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.74 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 2
Chains and sequence ranges Author chain G; PDBConstruct 1–59; UniProt 5–63

Proteinase-activated receptor 1

Homo sapiens

UniProt P25116

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 42–425 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) scFv16 × 1 Guanine nucleotide-binding protein G(q) subunit alpha chimera × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.74 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.

12 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAR1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain R; PDBConstruct 1–384; UniProt 42–425

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 9d4z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9d4z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9d4z
Deposition date deposition_date2024-08-13
Structure title titleCryoEM structure of PAR1 with endogenous tethered ligand
Keywords keywordsPAR2, endogenous ligand., IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier37.20
Radius of gyration Rg (electron density) rg_electron37.00
Forward intensity I(0) i0204448000.00
Molecular weight molecular_weight117450.0 kDa
Excluded volume excluded_volume147640 ų
Envelope volume envelope_volume190630 ų
Hydration-shell volume shell_volume43968 ų
Envelope diameter envelope_diameter122.3
Shell Rg shell_rg41.65
Envelope Rg envelope_rg36.85
Shape Rg shape_rg37.01
Total Rg total_rg37.26
Total atoms total_atoms8267
Residues n_residues1067
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 dmax118.5
Rg (real space) rg_real37.16
Rg uncertainty (real space) rg_real_error0.91
I(0) (real space) i0_real2.0440e+08
I(0) uncertainty (real space) i0_real_error3.5100e+06
Rg (reciprocal space) rg_reciprocal37.19
I(0) (reciprocal space) i0_reciprocal204500000.0000
Solution quality estimate total_estimate0.8956
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.6
Skewness Skewness skewness0.189
Kurtosis Kurtosis kurtosis-0.690
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44030000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.835

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)