7l1u

Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Peptide-Agonist Orexin B (OxB)

Method: ELECTRON MICROSCOPY Dmax: 124.8 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Engineered Guanine nucleotide-binding protein subunit alpha × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) single-chain antibody Fv fragment (svFv16) × 1 Hypocretin receptor type 2 × 1 (Q548Y0) Orexin × 1 (O43612) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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 11–349; 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–71 Not recorded Engineered Guanine nucleotide-binding protein subunit alpha × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) single-chain antibody Fv fragment (svFv16) × 1 Hypocretin receptor type 2 × 1 (Q548Y0) Orexin × 1 (O43612) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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 C; PDBConstruct 1–71; UniProt 1–71

Hypocretin receptor type 2

Homo sapiens

UniProt Q548Y0

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain R; UniProt 3–389 Not recorded Engineered Guanine nucleotide-binding protein 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) single-chain antibody Fv fragment (svFv16) × 1 Orexin × 1 (O43612) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q548Y0_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain R; PDBConstruct 9–364; UniProt 3–389

Orexin

OrganismNot specified

UniProt O43612

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain L; UniProt 70–97 Non-standard monomer:Yes (specific site not provided by mmCIF) Engineered Guanine nucleotide-binding protein 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) single-chain antibody Fv fragment (svFv16) × 1 Hypocretin receptor type 2 × 1 (Q548Y0) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OREX_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain L; PDBConstruct 1–28; UniProt 70–97

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 7l1u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7l1u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7l1u
Deposition date deposition_date2020-12-15
Structure title titleOrexin Receptor 2 (OX2R) in Complex with G Protein and Natural Peptide-Agonist Orexin B (OxB)
Keywords keywordsClass A GPCR, Orexin receptor 2, OX2R, membrane protein, Peptide agonist; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.13
Radius of gyration Rg (electron density) rg_electron38.02
Forward intensity I(0) i0227917000.00
Molecular weight molecular_weight124030.0 kDa
Excluded volume excluded_volume155920 ų
Envelope volume envelope_volume208680 ų
Hydration-shell volume shell_volume46970 ų
Envelope diameter envelope_diameter129.4
Shell Rg shell_rg42.32
Envelope Rg envelope_rg38.02
Shape Rg shape_rg38.03
Total Rg total_rg38.26
Total atoms total_atoms8723
Residues n_residues1148
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 dmax124.8
Rg (real space) rg_real38.09
Rg uncertainty (real space) rg_real_error1.24
I(0) (real space) i0_real2.2790e+08
I(0) uncertainty (real space) i0_real_error4.4390e+06
Rg (reciprocal space) rg_reciprocal38.12
I(0) (reciprocal space) i0_reciprocal227900000.0000
Solution quality estimate total_estimate0.8969
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.7
Skewness Skewness skewness0.209
Kurtosis Kurtosis kurtosis-0.613
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37360000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.906

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7l1uA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id7l1uB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

8. Citations (1)

9. Files and Curves (10)