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- PDB-5jqh: Structure of beta2 adrenoceptor bound to carazolol and inactive-s... -

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Basic information

Entry
Database: PDB / ID: 5jqh
TitleStructure of beta2 adrenoceptor bound to carazolol and inactive-state stabilizing nanobody, Nb60
Components
  • Endolysin,Beta-2 adrenergic receptor
  • Nanobody60, Nb60
Keywordssignaling protein / hydrolase/inhibitor / GPCR / Signaling / Nanobody / Allostery / HYDROLASE / hydrolase-inhibitor complex
Function / homology
Function and homology information


: / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure ...: / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / response to psychosocial stress / negative regulation of multicellular organism growth / adrenergic receptor signaling pathway / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / adenylate cyclase binding / smooth muscle contraction / potassium channel regulator activity / positive regulation of bone mineralization / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / viral release from host cell by cytolysis / bone resorption / activation of adenylate cyclase activity / response to cold / peptidoglycan catabolic process / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein serine/threonine kinase activity / cellular response to amyloid-beta / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / Clathrin-mediated endocytosis / lysozyme activity / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / cell surface receptor signaling pathway / lysosome / early endosome / receptor complex / endosome membrane / Ub-specific processing proteases / endosome / defense response to bacterium / apical plasma membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / nucleus / 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 / Lysozyme domain superfamily / 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 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Lysozyme-like domain superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-CAU / CHOLESTEROL / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsStaus, D.P. / Strachan, R.T. / Manglik, A. / Pani, B. / Kahsai, A.W. / Kim, T.H. / Wingler, L.M. / Ahn, S. / Chatterjee, A. / Masoudi, A. ...Staus, D.P. / Strachan, R.T. / Manglik, A. / Pani, B. / Kahsai, A.W. / Kim, T.H. / Wingler, L.M. / Ahn, S. / Chatterjee, A. / Masoudi, A. / Kruse, A.C. / Pardon, E. / Steyaert, J. / Weis, W.I. / Prosser, R.S. / Kobilka, B.K. / Costa, T. / Lefkowitz, R.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL70631 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS028471 United States
CitationJournal: Nature / Year: 2016
Title: Allosteric nanobodies reveal the dynamic range and diverse mechanisms of G-protein-coupled receptor activation.
Authors: Staus, D.P. / Strachan, R.T. / Manglik, A. / Pani, B. / Kahsai, A.W. / Kim, T.H. / Wingler, L.M. / Ahn, S. / Chatterjee, A. / Masoudi, A. / Kruse, A.C. / Pardon, E. / Steyaert, J. / Weis, W. ...Authors: Staus, D.P. / Strachan, R.T. / Manglik, A. / Pani, B. / Kahsai, A.W. / Kim, T.H. / Wingler, L.M. / Ahn, S. / Chatterjee, A. / Masoudi, A. / Kruse, A.C. / Pardon, E. / Steyaert, J. / Weis, W.I. / Prosser, R.S. / Kobilka, B.K. / Costa, T. / Lefkowitz, R.J.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endolysin,Beta-2 adrenergic receptor
B: Endolysin,Beta-2 adrenergic receptor
D: Nanobody60, Nb60
C: Nanobody60, Nb60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,8318
Polymers134,4614
Non-polymers1,3704
Water00
1
A: Endolysin,Beta-2 adrenergic receptor
C: Nanobody60, Nb60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9154
Polymers67,2302
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-9 kcal/mol
Surface area24310 Å2
MethodPISA
2
B: Endolysin,Beta-2 adrenergic receptor
D: Nanobody60, Nb60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9154
Polymers67,2302
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-9 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.924, 164.486, 218.749
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 53699.281 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-161, UNP RESIDEUS 30-348
Mutation: C919T, C962A, M1096T, M1098T, N1187E, C1265A,C919T, C962A, M1096T, M1098T, N1187E, C1265A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Plasmid: pVL1392 / Gene: ADRB2, ADRB2R, B2AR / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00720, UniProt: P07550, lysozyme
#2: Antibody Nanobody60, Nb60


Mass: 13531.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CAU / (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol / (S)-Carazolol


Mass: 298.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N2O2
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O

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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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5 / Details: 100 mM HEPES pH 7.5, 20 mM EDTA, and 19-23% PEG300

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2014
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: 3.2→32.9 Å / Num. obs: 26778 / % possible obs: 98.6 % / Redundancy: 5.5 % / CC1/2: 0.986 / Rmerge(I) obs: 0.175 / Net I/σ(I): 5.3
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 1.5 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RH1

2rh1


Resolution: 3.2→32.867 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.67
RfactorNum. reflection% reflectionSelection details
Rfree0.2903 1967 7.35 %Random selection
Rwork0.2465 ---
obs0.2497 26778 98.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→32.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7601 0 100 0 7701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037893
X-RAY DIFFRACTIONf_angle_d0.42910808
X-RAY DIFFRACTIONf_dihedral_angle_d10.3254621
X-RAY DIFFRACTIONf_chiral_restr0.0361299
X-RAY DIFFRACTIONf_plane_restr0.0021332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.43871320.38311665X-RAY DIFFRACTION95
3.28-3.36860.39251360.3551722X-RAY DIFFRACTION96
3.3686-3.46760.40961360.32681705X-RAY DIFFRACTION98
3.4676-3.57940.35911370.29491748X-RAY DIFFRACTION99
3.5794-3.70720.341410.28151764X-RAY DIFFRACTION99
3.7072-3.85540.34991370.271735X-RAY DIFFRACTION99
3.8554-4.03060.35331410.25731786X-RAY DIFFRACTION99
4.0306-4.24270.26321390.21931739X-RAY DIFFRACTION99
4.2427-4.50780.23861400.20381787X-RAY DIFFRACTION99
4.5078-4.85490.26231450.20871814X-RAY DIFFRACTION99
4.8549-5.34160.25821410.22411775X-RAY DIFFRACTION99
5.3416-6.11020.32461440.26771809X-RAY DIFFRACTION99
6.1102-7.6820.31041450.26431841X-RAY DIFFRACTION99
7.682-32.86830.23881530.22081921X-RAY DIFFRACTION97
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)
17.24062.4502-6.12532.480.49359.1567-0.49281.524-0.2548-2.91091.5743-0.7331-0.86130.162-0.80331.8546-0.12290.18971.4883-0.44120.94416.348-4.187-92.5544
22.94272.44880.37189.58387.63948.983-0.18961.0293-1.277-1.631-0.23560.9596-1.0082-1.12510.53141.9984-0.3355-0.06291.5442-0.28651.32794.3742-7.1053-91.807
31.8140.47910.39743.3792-0.08932.7325-0.02360.32410.1056-1.07470.0245-0.18280.0726-0.00150.02041.20870.1221-0.04550.87430.06320.60467.2748-31.1263-52.2111
47.0773.53842.49837.34341.03022.1005-0.05091.23421.1945-1.5152-0.57320.3158-0.4063-0.68680.33941.0620.3234-0.08330.93570.080.73918.2005-17.5867-35.5809
54.67143.0386-1.05796.6351-2.24226.52730.3238-0.30420.53090.3594-0.05710.1318-2.021-0.8787-0.29051.87280.24340.03771.0229-0.13030.7837.7096-3.7475-17.2235
61.5916-1.3092-0.11673.2873-1.69591.7914-0.021-0.33730.04420.94650.163-0.2269-0.1169-0.1203-0.13831.7727-0.0727-0.24991.16330.05460.707610.839920.4021-54.91
75.0801-2.5014-1.79566.87832.84392.1498-0.26630.0292-0.28060.452-0.1640.57540.1355-0.27860.39231.1685-0.1316-0.14070.81740.01440.6259-0.062516.9699-63.3032
82222222.111218.3236-9.3206-11.4292-1.5603-6.97753.6124-16.2799-0.56361.2539-0.15980.57732.8268-0.12081.701921.5231-1.3184-74.452
95.0943-5.1439-4.81488.79124.05424.53171.5972.04593.00750.5456-0.0845-1.29620.8162-1.3785-1.56571.1114-0.0356-0.01861.36910.2251.107816.134923.0516-107.7209
105.7995-3.0661-6.16674.72364.32817.35160.4193-0.70.4410.09890.4442-0.0241-0.95361.3073-0.49260.9819-0.0295-0.191.24210.06980.671415.805524.406-97.353
116.76740.24722.15379.08681.34665.09831.3816-0.6186-1.1641-1.47570.6610.52381.4894-0.8047-1.77431.1270.0383-0.33080.74070.1041.23421.983513.7203-99.4001
122.58142.7679-0.71975.5572-5.24867.90990.7688-1.1355-0.47970.8879-0.0873-0.6960.57122.1381-0.60161.64380.2961-0.36241.3941-0.19030.954527.992823.3714-94.8597
137.28830.24321.64443.4468-2.8174.28350.14810.5205-0.3438-0.9043-0.5001-0.4219-0.80040.13470.40521.2664-0.0921-0.14611.0586-0.10110.645320.557524.1586-100.8269
143.6280.5567-2.40954.5157-3.18923.3382-0.09450.3679-0.62980.2898-0.2366-0.25260.64-0.3010.23041.1913-0.0091-0.15910.7546-0.09720.751712.151517.294-95.6909
159.56023.03485.74185.81623.69837.0460.2673-1.2847-0.54580.9494-0.13690.2974-0.9759-1.10070.00321.21140.043-0.11940.77250.03490.485713.0529-35.6721-0.4478
161.41463.19642.16497.16054.85213.2793-0.0673-0.0723-1.50980.95360.4534-0.85190.23761.05270.16020.2136-0.1707-0.02721.47810.52360.89314.1021-39.8292-4.2395
176.6542-0.20394.29142.4102-2.19494.5211.79740.7674-1.7279-1.3840.22421.47292.4545-0.0531-1.55371.7368-0.0318-1.14191.05590.28111.51498.6757-40.2819-19.684
188.61456.57517.08495.50234.99876.16950.1031-0.2091.7627-0.696-0.22280.04930.4068-0.23450.11460.83050.41220.07831.4676-0.00920.673716.6509-30.0734-9.007
194.1678-0.1173-4.24744.99064.37588.5320.3915-0.38280.83760.93541.34540.406-0.19450.478-0.23120.5866-0.1425-0.51061.17760.42250.569219.5279-25.8226-7.7203
205.05252.76095.22257.05714.05116.9481-0.82351.12360.305-1.19090.4763-0.7968-0.80382.0341-0.01820.5855-0.3892-0.28581.67950.34521.059425.7817-34.6586-11.9848
219.41362.3257-3.07688.8954-4.6012.77340.02190.03480.0963-0.7906-0.45360.73140.80670.59450.32570.7432-0.144-0.27710.97950.16640.847516.5971-42.7376-11.5251
227.2297-1.37393.15516.34590.04964.3331-0.2739-1.3009-0.0314-0.61050.3913-0.8371-0.1376-0.6251-0.01850.96970.095-0.17811.40180.2370.609422.0065-35.7759-1.4441
230.36570.44470.89970.87111.52894.3105-0.4705-0.7070.32430.77460.06530.0571-0.4278-0.27020.3660.88660.0141-0.1991.22050.13540.875112.7317-30.5558-10.1365
249.4634-0.55646.12864.8233-1.84714.4547-0.8196-0.93760.25350.7291-0.9172-1.0993-1.10690.37781.48820.57490.0129-0.12690.67430.13790.73647.2549-28.6273-19.228
252.20820.378-1.31589.81451.12090.9641-0.3053-2.6156-0.47140.9752-0.073-1.1037-0.13560.11810.19781.18840.2960.15341.8612-0.17740.342119.3474-30.77888.0234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 867 through 970 )
2X-RAY DIFFRACTION2chain 'A' and (resid 971 through 1023 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1024 through 1320 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1321 through 1343 )
5X-RAY DIFFRACTION5chain 'B' and (resid 866 through 1023 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1024 through 1208 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1209 through 1342 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1343 through 1343 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 16 )
10X-RAY DIFFRACTION10chain 'D' and (resid 17 through 39 )
11X-RAY DIFFRACTION11chain 'D' and (resid 40 through 51 )
12X-RAY DIFFRACTION12chain 'D' and (resid 52 through 66 )
13X-RAY DIFFRACTION13chain 'D' and (resid 67 through 100 )
14X-RAY DIFFRACTION14chain 'D' and (resid 101 through 117 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 16 )
16X-RAY DIFFRACTION16chain 'C' and (resid 17 through 25 )
17X-RAY DIFFRACTION17chain 'C' and (resid 26 through 32 )
18X-RAY DIFFRACTION18chain 'C' and (resid 33 through 40 )
19X-RAY DIFFRACTION19chain 'C' and (resid 41 through 51 )
20X-RAY DIFFRACTION20chain 'C' and (resid 52 through 66 )
21X-RAY DIFFRACTION21chain 'C' and (resid 67 through 76 )
22X-RAY DIFFRACTION22chain 'C' and (resid 77 through 90 )
23X-RAY DIFFRACTION23chain 'C' and (resid 91 through 100 )
24X-RAY DIFFRACTION24chain 'C' and (resid 101 through 112 )
25X-RAY DIFFRACTION25chain 'C' and (resid 113 through 120 )

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