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- PDB-9rkh: Dark structure of beta-2 Adrenergic receptor with photoazolol in ... -

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Basic information

Entry
Database: PDB / ID: 9rkh
TitleDark structure of beta-2 Adrenergic receptor with photoazolol in Dark state recorded at LCLS
ComponentsBeta-2 adrenergic receptor,Endolysin
KeywordsMEMBRANE PROTEIN / GPCR / 7TM / Beta 2 / ADRENERGIC / LIPIDIC CUBIC PHASE / LIPIDIC / PHOTO-SWITCHABLE COMPOUNDS / PHOTOAZOLOL-1 / TIME RESOLVE CRYSTALLOGRAPHY
Function / homology
Function and homology information


beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / AMPA selective glutamate receptor signaling pathway / heat generation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine binding / Adrenoceptors / negative regulation of smooth muscle contraction ...beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / AMPA selective glutamate receptor signaling pathway / heat generation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine binding / Adrenoceptors / negative regulation of smooth muscle contraction / positive regulation of cardiac muscle cell contraction / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / adrenergic receptor signaling pathway / diet induced thermogenesis / response to psychosocial stress / endosome to lysosome transport / positive regulation of cAMP/PKA signal transduction / smooth muscle contraction / negative regulation of cardiac muscle cell apoptotic process / adenylate cyclase binding / potassium channel regulator activity / bone resorption / positive regulation of bone mineralization / viral release from host cell by cytolysis / neuronal dense core vesicle / intercellular bridge / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / peptidoglycan catabolic process / positive regulation of cardiac muscle cell apoptotic process / receptor-mediated endocytosis / brown fat cell differentiation / response to cold / clathrin-coated endocytic vesicle membrane / cellular response to amyloid-beta / cell wall macromolecule catabolic process / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / lysozyme / lysozyme activity / mitotic spindle / Cargo recognition for clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / Clathrin-mediated endocytosis / microtubule cytoskeleton / transcription by RNA polymerase II / G alpha (s) signalling events / host cell cytoplasm / early endosome / positive regulation of MAPK cascade / cell surface receptor signaling pathway / lysosome / signaling receptor complex / defense response to bacterium / endosome / endosome membrane / apical plasma membrane / Ub-specific processing proteases / cilium / ciliary basal body / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme-like domain superfamily ...Beta 2 adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme-like domain superfamily / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PALMITIC ACID / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBertrand, Q. / Stipp, R. / Glover, H. / Stierli, F. / Siedel, H.P. / Mous, S. / Kepa, M. / Weinert, T. / Standfuss, J.
Funding supportEuropean Union, Switzerland, 4items
OrganizationGrant numberCountry
Innosuisse42711.1 IP-LSEuropean Union
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation310030_197674 Switzerland
Swiss National Science FoundationCRSII5_213507 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: Structural Mechanism of an Efficacy Photoswitch Targeting the beta 2 -adrenergic Receptor.
Authors: Stipp, R. / Bertrand, Q. / Trabuco, M. / Duran-Corbera, A. / Ignazzitto, M.T. / Glover, H. / Stierli, F. / Catena, J. / Carrillo, M. / Hartmann, S. / Seidel, H.P. / Mulder, M. / Mason, T. / ...Authors: Stipp, R. / Bertrand, Q. / Trabuco, M. / Duran-Corbera, A. / Ignazzitto, M.T. / Glover, H. / Stierli, F. / Catena, J. / Carrillo, M. / Hartmann, S. / Seidel, H.P. / Mulder, M. / Mason, T. / Kondo, Y. / Wranik, M. / Appleby, M. / Sager, C. / Sierra, R. / Gate, G. / Schleissner, P. / Cheng, X. / Weinert, T. / Cheng, R. / Mous, S. / Beale, J.H. / Kepa, M. / Llebaria, A. / Hennig, M. / Rovira, X. / Standfuss, J.
History
DepositionJun 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.1May 6, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,69822
Polymers50,5281
Non-polymers6,17021
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.940, 172.230, 41.230
Angle α, β, γ (deg.)90.000, 106.200, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-2 adrenergic receptor,Endolysin / Beta-2 adrenoreceptor / Beta-2 adrenoceptor / Lysis protein / Lysozyme / Muramidase


Mass: 50528.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ADRB2, ADRB2R, B2AR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P07550, UniProt: P00720, lysozyme

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Non-polymers , 9 types, 47 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#6: Chemical ChemComp-A1JHU / ~{N}-[4-[(~{E})-[2-[(2~{S})-2-oxidanyl-3-(propan-2-ylamino)propoxy]phenyl]diazenyl]phenyl]ethanamide


Mass: 370.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N4O3
#7: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.47 %
Crystal growTemperature: 289 K / Method: lipidic cubic phase
Details: 100 mM tri-sodium citrate (pH= 6.2), 245 mM Li2SO4, 32% PEG 350 MME, 10 uM photoazolol-1

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.4089 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4089 Å / Relative weight: 1
ReflectionResolution: 2.5→28.33 Å / Num. obs: 25813 / % possible obs: 100 % / Redundancy: 153 % / CC star: 0.996 / R split: 0.123 / Net I/σ(I): 6.43
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 104 % / Mean I/σ(I) obs: 0.54 / Num. unique obs: 2609 / CC star: 0.767 / R split: 1.53 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.33 Å / SU ML: 0.455 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.6929
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 2010 7.79 %
Rwork0.1931 23803 -
obs0.195 25813 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 318 26 3895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493954
X-RAY DIFFRACTIONf_angle_d0.89855309
X-RAY DIFFRACTIONf_chiral_restr0.0374593
X-RAY DIFFRACTIONf_plane_restr0.0159623
X-RAY DIFFRACTIONf_dihedral_angle_d17.95971457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.46871510.421669X-RAY DIFFRACTION97.85
2.56-2.630.36811320.3831689X-RAY DIFFRACTION99.51
2.63-2.710.36481570.32051696X-RAY DIFFRACTION100
2.71-2.80.29621350.28091689X-RAY DIFFRACTION100
2.8-2.90.2711410.26561705X-RAY DIFFRACTION100
2.9-3.010.27891380.26081704X-RAY DIFFRACTION100
3.01-3.150.27881530.2461703X-RAY DIFFRACTION100
3.15-3.310.25081330.21021700X-RAY DIFFRACTION99.95
3.31-3.520.22381530.19071688X-RAY DIFFRACTION100
3.52-3.790.21251350.17071713X-RAY DIFFRACTION100
3.79-4.170.20631520.14961703X-RAY DIFFRACTION100
4.17-4.780.16171350.14841707X-RAY DIFFRACTION100
4.78-60.1931490.17781716X-RAY DIFFRACTION100
6.01-28.330.18171460.17241721X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.600426865441.978560302220.3343732861075.54220352720.7405282229561.24840351131-0.06481176748190.264924777369-0.475217760312-0.4567449225630.1693087084120.2621646168850.278950807951-0.100965371169-0.1050756935840.70229855758-0.078598175288-0.0367318436180.634653053493-0.06225188608970.54771696578319.361066178716.21292209093.14447765132
21.19682398048-0.409661026977-0.1043149167817.421435759371.671957959011.050181656970.1069182687930.1212475277020.262210247641-0.460001209391-0.201193715930.259352607146-0.434704145773-0.2147229274980.09739488997770.6433357434410.0268545110395-0.005696422065350.6397721839960.001370167046740.39984100410525.399592845857.114040787813.6228420727
32.938699147970.3369938000722.059685784462.97095782997-0.2897015939074.16290651225-0.14267078773-0.1157943787220.201983468204-0.0621517831309-0.1015403841960.0575035699277-0.0990232093656-0.1850123733440.2397366179310.4943473847340.0301176913280.07337604369020.589339048489-0.0194422161810.35175391814131.368038332358.147906860731.3625399371
42.447130909910.600830841180.6762239575785.06370696474-0.0248302768042.287742356130.0924255895318-0.270795616339-0.3875624258480.4405560358870.07208544467340.3980536427390.0820884875725-0.434228750961-0.1718965357750.517314823712-0.1265056132410.01715598072120.63889857549-0.00258577792880.50971380807918.97335693321.514176528814.2908666542
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 29 through 208 )29 - 2081 - 180
22chain 'A' and (resid 209 through 259 )209 - 259181 - 260
33chain 'A' and (resid 260 through 266 )260 - 266261 - 366
44chain 'A' and (resid 267 through 342 )267 - 342367 - 442

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