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- PDB-4qkx: Structure of beta2 adrenoceptor bound to a covalent agonist and a... -

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Basic information

Entry
Database: PDB / ID: 4qkx
TitleStructure of beta2 adrenoceptor bound to a covalent agonist and an engineered nanobody
Components
  • Beta-2 adrenergic receptor
  • R9 protein
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / 7-transmembrane helices / Signal transduction / G proteins / Membrane / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / AMPA selective glutamate receptor signaling pathway / norepinephrine binding / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction ...positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / AMPA selective glutamate receptor signaling pathway / norepinephrine binding / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of multicellular organism growth / adrenergic receptor signaling pathway / response to psychosocial stress / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / bone resorption / positive regulation of bone mineralization / potassium channel regulator activity / brown fat cell differentiation / intercellular bridge / viral release from host cell by cytolysis / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / peptidoglycan catabolic process / receptor-mediated endocytosis / response to cold / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / cell wall macromolecule catabolic process / mitotic spindle / lysozyme / lysozyme activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / amyloid-beta binding / positive regulation of cold-induced thermogenesis / microtubule cytoskeleton / G alpha (s) signalling events / transcription by RNA polymerase II / host cell cytoplasm / early endosome / lysosome / receptor complex / cell surface receptor signaling pathway / positive regulation of MAPK cascade / endosome / endosome membrane / Ub-specific processing proteases / defense response to bacterium / ciliary basal body / cilium / apical plasma membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme ...Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / G-protein coupled receptors family 1 signature. / Lysozyme-like domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-35V / Endolysin / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsWeichert, D. / Kruse, A.C. / Manglik, A. / Hiller, C. / Zhang, C. / Huebner, H. / Kobilka, B.K. / Gmeiner, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Covalent agonists for studying G protein-coupled receptor activation.
Authors: Weichert, D. / Kruse, A.C. / Manglik, A. / Hiller, C. / Zhang, C. / Hubner, H. / Kobilka, B.K. / Gmeiner, P.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref / struct_ref_seq_dif
Item: _struct_ref.pdbx_align_begin / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor
B: R9 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8115
Polymers66,3852
Non-polymers4253
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-49 kcal/mol
Surface area27790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.558, 67.211, 301.269
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-2 adrenergic receptor / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


Mass: 53436.035 Da / Num. of mol.: 1
Mutation: C919T, C962A, H1093C, M1096T, M1098T, N1187E, C1265A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126, ADRB2, ADRB2R, B2AR / Plasmid: PVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: D9IEF7, UniProt: P07550, UniProt: P00720*PLUS, lysozyme
#2: Antibody R9 protein


Mass: 12949.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Gene: r9 / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-35V / 4-[(1R)-1-hydroxy-2-({2-[3-methoxy-4-(2-sulfanylethoxy)phenyl]ethyl}amino)ethyl]benzene-1,2-diol


Mass: 379.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25NO5S
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.45 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.8
Details: 24-27 % PEG400, 100 mM Tris pH 7.8 to pH 8.4, 5-10 mM Sodium formate, lipidic cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2013
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.3→33.3 Å / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.29 Å2

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1241refinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing
RefinementResolution: 3.3→33.26 Å / FOM work R set: 0.7753 / SU ML: 0.52 / σ(F): 1.34 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2795 2298 10.03 %
Rwork0.2356 20610 -
obs0.2401 22908 78.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.6 Å2 / Biso mean: 101.1 Å2 / Biso min: 57.38 Å2
Refinement stepCycle: LAST / Resolution: 3.3→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 0 28 0 4462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054579
X-RAY DIFFRACTIONf_angle_d0.6346220
X-RAY DIFFRACTIONf_chiral_restr0.042719
X-RAY DIFFRACTIONf_plane_restr0.003777
X-RAY DIFFRACTIONf_dihedral_angle_d9.2541563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.37170.4041120.34451049116165
3.3717-3.45010.40211310.3231121125269
3.4501-3.53630.36041420.321226136873
3.5363-3.63180.35961240.30271209133374
3.6318-3.73850.35931440.29991202134674
3.7385-3.8590.32531390.2781227136674
3.859-3.99670.28181300.25511225135575
3.9967-4.15640.26961600.23891379153983
4.1564-4.34520.24341530.22321276142981
4.3452-4.57370.27041600.21051370153083
4.5737-4.85950.23671430.20891366150984
4.8595-5.23340.24821520.20641383153583
5.2334-5.75760.27061440.22341362150684
5.7576-6.58510.27961490.23691391154084
6.5851-8.27530.25481540.20171428158286
8.2753-33.26160.23491610.18571396155786
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)
13.99363.5925-0.55863.3508-0.78921.7250.14720.3235-0.37930.12550.0374-0.47450.02790.0863-0.16980.80960.022-0.05990.40960.04470.938416.2789-4.4824-76.8296
21.80310.0588-0.06061.53361.04295.97890.0622-0.26150.0796-0.04410.00840.0116-0.11840.3954-0.04280.7167-0.0443-0.02340.90780.04970.57734.0735-20.5815-38.8384
34.12131.7466-2.61475.0597-3.9293.49180.5618-0.88530.41710.80730.1327-0.0167-1.19720.144-0.77451.0378-0.03820.11061.4228-0.0750.73841.2139-11.19353.961
42.7039-1.41534.51359.4235-2.87787.55740.6471-1.3592-0.47830.7407-0.12550.35270.08761.0877-0.37040.73250.0108-0.0321.2008-0.09620.69181.7449-18.9883-0.7522
53.1353-3.8962.70777.3385-1.36933.9344-0.5914-0.3112-0.28660.60720.0291-0.1180.9604-1.43780.49421.026-0.23790.11031.73010.08140.62631.5307-23.5042-0.6267
62.66421.2231-3.17816.2136-0.33934.0123-0.1421-0.8735-0.80531.4674-0.51330.391-0.1809-0.37750.71081.022-0.2037-0.00411.45370.07120.6413-8.2465-22.8324-0.5262
75.96350.6781-0.98366.36072.6792.0612-0.0681-0.78151.0379-0.92230.2150.0592-0.5796-0.604-0.29621.0395-0.008-0.06031.18880.12150.5784-7.2976-10.45950.5332
86.8276-5.12680.86535.152-0.50352.30370.0564-0.0637-0.47570.20270.56470.5523-0.7473-1.0569-0.6430.9529-0.01210.03781.05420.18810.6885-3.6585-20.57199.3977
95.7172-4.13073.86358.8667-6.90875.5001-0.2659-0.7285-0.16930.25560.7260.1783-0.56770.173-0.57780.7261-0.0773-0.08061.4471-0.11890.74324.4522-17.0315-0.7249
103.9954-3.6862-3.43623.58834.20148.60410.2308-0.18020.6409-0.06930.13440.30930.8707-0.1701-0.25710.7204-0.17270.14240.71360.02790.96013.4011-14.0206-18.3432
114.8033.1108-3.31469.6472-7.29399.2756-0.3141-0.2421-0.10250.9926-0.9925-0.9966-0.88620.44841.37130.80180.1465-0.08712.2145-0.15990.85116.7184-17.36863.8632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 858 through 1027 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1028 through 1342 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 33 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 34 through 42 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 54 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 55 through 68 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 69 through 78 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 92 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 101 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 102 through 108 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 122 )B0

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