9l3y

Cryo-EM structure of the G-protein coupled receptor 1 (GPR1) in complex with chemerin and Gi1

Method: ELECTRON MICROSCOPY Dmax: 141.7 Å Quality: GOOD

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

Chemerin-like receptor 2

Homo sapiens

UniProt P46091

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 1–322 Not recorded Retinoic acid receptor responder protein 2 × 1 (Q99969) 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) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CML2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 1–322; UniProt 1–322

Retinoic acid receptor responder protein 2

Homo sapiens

UniProt Q99969

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 L; UniProt 21–157 Not recorded Chemerin-like receptor 2 × 1 (P46091) 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) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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.

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RARR2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain L; PDBConstruct 1–137; UniProt 21–157

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 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–354 Mutation:S47C,G202T,G203A,E245A,A326S Chemerin-like receptor 2 × 1 (P46091) Retinoic acid receptor responder protein 2 × 1 (Q99969) 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) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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 3
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 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 1–340 Not recorded Chemerin-like receptor 2 × 1 (P46091) Retinoic acid receptor responder protein 2 × 1 (Q99969) 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) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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 4
Chains and sequence ranges Author chain B; PDBConstruct 1–340; UniProt 1–340

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 C; UniProt 1–71 Not recorded Chemerin-like receptor 2 × 1 (P46091) Retinoic acid receptor responder protein 2 × 1 (Q99969) 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) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.60 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 5
Chains and sequence ranges Author chain C; 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 9l3y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9l3y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9l3y
Deposition date deposition_date2024-12-19
Structure title titleCryo-EM structure of the G-protein coupled receptor 1 (GPR1) in complex with chemerin and Gi1
Keywords keywordsGPCR, GPR1, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier41.18
Radius of gyration Rg (electron density) rg_electron40.97
Forward intensity I(0) i0159455000.00
Molecular weight molecular_weight104690.0 kDa
Excluded volume excluded_volume131810 ų
Envelope volume envelope_volume183570 ų
Hydration-shell volume shell_volume39986 ų
Envelope diameter envelope_diameter150.5
Shell Rg shell_rg42.17
Envelope Rg envelope_rg41.97
Shape Rg shape_rg40.99
Total Rg total_rg40.98
Total atoms total_atoms7383
Residues n_residues993
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 dmax141.7
Rg (real space) rg_real41.66
Rg uncertainty (real space) rg_real_error1.55
I(0) (real space) i0_real1.5950e+08
I(0) uncertainty (real space) i0_real_error3.0280e+06
Rg (reciprocal space) rg_reciprocal41.18
I(0) (reciprocal space) i0_reciprocal159400000.0000
Solution quality estimate total_estimate0.7818
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.6
Skewness Skewness skewness0.596
Kurtosis Kurtosis kurtosis-0.346
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15270000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.683; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.678; Smooth: 0.433

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)