9rkf

Dark structure of beta-2 Adrenergic receptor with photoazolol in Dark state recorded at SwissFEL

Method: X-RAY DIFFRACTION Dmax: 99.0 Å Quality: GOOD

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

Beta-2 adrenergic receptor,Endolysin

Homo sapiens

UniProt P00720

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 Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 2–162 Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 5 CLR CHOLESTEROL × 3 12P DODECAETHYLENE GLYCOL × 3 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 5 1PE PENTAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 A1JHU ~{N}-[4-[(~{E})-[2-[(2~{S})-2-oxidanyl-3-(propan-2-ylamino)propoxy]phenyl]diazenyl]phenyl]ethanamide × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;289 K;100mM tri-sodium citrate pH= 6.2, 245mM Li2SO4, 32% PEG 350 MME, 10uM photoazolol-1 Resolution 2.45 Å R-free 0.219

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.

721 other PDB entries and 846 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENLYS_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 204–364; UniProt 2–162

Beta-2 adrenergic receptor,Endolysin

Homo sapiens

UniProt P07550

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 Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 28–230 Chain A; UniProt 264–342 Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 5 CLR CHOLESTEROL × 3 12P DODECAETHYLENE GLYCOL × 3 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 5 1PE PENTAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 A1JHU ~{N}-[4-[(~{E})-[2-[(2~{S})-2-oxidanyl-3-(propan-2-ylamino)propoxy]phenyl]diazenyl]phenyl]ethanamide × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;289 K;100mM tri-sodium citrate pH= 6.2, 245mM Li2SO4, 32% PEG 350 MME, 10uM photoazolol-1 Resolution 2.45 Å R-free 0.219

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.

143 other PDB entries and 145 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADRB2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–203; UniProt 28–230 Author chain A; PDBConstruct 365–443; UniProt 264–342

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 9rkf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9rkf
Deposition date deposition_date2025-06-13
Structure title titleDark structure of beta-2 Adrenergic receptor with photoazolol in Dark state recorded at SwissFEL
Keywords keywords;GPCR, 7TM, Beta 2, ADRENERGIC, LIPIDIC CUBIC PHASE, LIPIDIC, MEMBRANE PROTEIN, PHOTO-SWITCHABLE COMPOUNDS, PHOTOAZOLOL-1, TIME RESOLVE CRYSTALLOGRAPHY ;; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.25
Radius of gyration Rg (electron density) rg_electron29.44
Forward intensity I(0) i043118400.00
Molecular weight molecular_weight55042.0 kDa
Excluded volume excluded_volume70199 ų
Envelope volume envelope_volume90054 ų
Hydration-shell volume shell_volume27183 ų
Envelope diameter envelope_diameter101.3
Shell Rg shell_rg34.65
Envelope Rg envelope_rg29.39
Shape Rg shape_rg29.42
Total Rg total_rg30.10
Total atoms total_atoms7633
Residues n_residues442
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 dmax99.0
Rg (real space) rg_real30.49
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real4.3120e+07
I(0) uncertainty (real space) i0_real_error6.0720e+05
Rg (reciprocal space) rg_reciprocal30.39
I(0) (reciprocal space) i0_reciprocal43120000.0000
Solution quality estimate total_estimate0.8558
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary26.7
Skewness Skewness skewness0.452
Kurtosis Kurtosis kurtosis-0.556
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10110000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.747; Smooth: 0.856

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

8. Citations (1)

9. Files and Curves (10)