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- PDB-3kj6: Crystal structure of a Methylated beta2 Adrenergic Receptor-Fab c... -

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Basic information

Entry
Database: PDB / ID: 3kj6
TitleCrystal structure of a Methylated beta2 Adrenergic Receptor-Fab complex
Components
  • Beta-2 adrenergic receptor
  • Fab heavy chain
  • Fab light chain
KeywordsSIGNALING PROTEIN / transmembrane helices / Cell membrane / Disulfide bond / G-protein coupled receptor / Glycoprotein / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Polymorphism / Receptor / Transducer / Transmembrane
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 / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of autophagosome maturation / 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 / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of autophagosome maturation / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / 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 / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / 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 / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (s) signalling events / transcription by RNA polymerase II / positive regulation of MAPK cascade / lysosome / early endosome / receptor complex / cell surface receptor signaling pathway / endosome / endosome membrane / Ub-specific processing proteases / 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 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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) ...Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / 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) / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBokoch, M.P. / Zou, Y. / Rasmussen, S.G.F. / Liu, C.W. / Nygaard, R. / Rosenbaum, D.M. / Fung, J.J. / Choi, H.-J. / Thian, F.S. / Kobilka, T.S. ...Bokoch, M.P. / Zou, Y. / Rasmussen, S.G.F. / Liu, C.W. / Nygaard, R. / Rosenbaum, D.M. / Fung, J.J. / Choi, H.-J. / Thian, F.S. / Kobilka, T.S. / Puglisi, J.D. / Weis, W.I. / Pardo, L. / Prosser, S. / Mueller, L. / Kobilka, B.K.
CitationJournal: Nature / Year: 2010
Title: Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor.
Authors: Bokoch, M.P. / Zou, Y. / Rasmussen, S.G. / Liu, C.W. / Nygaard, R. / Rosenbaum, D.M. / Fung, J.J. / Choi, H.J. / Thian, F.S. / Kobilka, T.S. / Puglisi, J.D. / Weis, W.I. / Pardo, L. / ...Authors: Bokoch, M.P. / Zou, Y. / Rasmussen, S.G. / Liu, C.W. / Nygaard, R. / Rosenbaum, D.M. / Fung, J.J. / Choi, H.J. / Thian, F.S. / Kobilka, T.S. / Puglisi, J.D. / Weis, W.I. / Pardo, L. / Prosser, R.S. / Mueller, L. / Kobilka, B.K.
History
DepositionNov 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_mutation / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor
L: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6044
Polymers88,5083
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)338.600, 48.600, 88.900
Angle α, β, γ (deg.)90.000, 104.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 41369.020 Da / Num. of mol.: 1 / Mutation: N187E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550
#2: Antibody Fab light chain


Mass: 23902.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody Fab heavy chain


Mass: 23236.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
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: 4 Å3/Da / Density % sol: 69.27 %
Crystal growTemperature: 298 K / Method: bicelles, vapor diffusion / pH: 7
Details: AmSO4, pH 7, bicelles, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 19946 / % possible obs: 98.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.117 / Χ2: 1.558 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.4-3.523.60.38318190.71890.2
3.52-3.664.30.35218970.896.4
3.66-3.834.90.31119850.87298.9
3.83-4.035.60.2720061.04499.4
4.03-4.285.80.21319961.45799.8
4.28-4.6160.16320121.70299.9
4.61-5.0860.13220251.87899.7
5.08-5.8160.12220361.85199.9
5.81-7.3260.10320581.801100
7.32-505.70.06221122.51798.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→44.409 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.799 / SU ML: 0.33 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 1864 9.79 %
Rwork0.238 --
obs0.242 19042 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 119.223 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 562.31 Å2 / Biso mean: 144.969 Å2 / Biso min: 51.18 Å2
Baniso -1Baniso -2Baniso -3
1--11.73 Å20 Å210.72 Å2
2--11.602 Å2-0 Å2
3----0.035 Å2
Refinement stepCycle: LAST / Resolution: 3.4→44.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4969 0 5 0 4974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035088
X-RAY DIFFRACTIONf_angle_d0.6696919
X-RAY DIFFRACTIONf_chiral_restr0.042802
X-RAY DIFFRACTIONf_plane_restr0.003869
X-RAY DIFFRACTIONf_dihedral_angle_d16.3311746
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.4920.2931350.2681137127282.28
3.492-3.5950.2661110.2561177128888.58
3.595-3.7110.2811440.2531281142592.23
3.711-3.8430.2791470.2291248139594.38
3.843-3.9970.2861570.231314147196.33
3.997-4.1790.2631560.2111332148898.22
4.179-4.3990.2071530.1921368152199.22
4.399-4.6740.2481600.1841308146899.06
4.674-5.0350.2111410.1831383152499.28
5.035-5.5410.2471400.21380152099.54
5.541-6.340.2881410.2371406154799.42
6.34-7.9810.3081290.2521416154599.81
7.981-44.4130.2821500.2641428157897.11
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)
1-4.6032-2.3268-3.1854-4.3464-0.70520.6586-0.12450.3235-0.13140.6725-1.0954-0.2915-0.62060.20590.99970.6752-0.1732-0.03420.7989-0.61253.035225.039738.471342.378
21.0547-0.4899-0.84070.5994-0.1266-1.0892-0.483-0.71791.23970.18540.3520.19780.15950.59980.2010.7164-0.19910.01731.5075-0.30872.863224.604645.536848.4296
3-0.38340.55450.84571.8729-1.0988-0.10181.69940.8643-0.67890.0369-1.49961.97280.1142-0.2409-0.13280.7750.2289-0.26981.8231-0.67682.224329.180657.211850.9754
48.9951-4.00220.7346.80930.53292.66910.2058-0.8124-0.02830.0694-0.46981.2363-0.72610.6089-0.02181.1877-0.05140.52171.3851-0.03941.718724.807454.370659.2464
50.4770.3437-0.18563.07861.06932.3541-0.5638-0.27220.0947-0.9087-0.62410.2279-0.26330.38580.5890.82360.0584-0.44320.5905-0.41890.514640.519863.790843.0775
6-1.17210.6583-0.11812.3415-0.66970.7611-0.18130.25570.26190.0698-0.51271.32720.271-0.87980.67911.31540.10.02612.0932-0.40171.748332.440856.462839.6897
71.61580.2620.40831.0424-1.11532.2741-0.4893-0.34750.05080.5094-0.3919-0.6606-0.70240.50380.4841.1562-0.13820.22591.8727-0.75492.32530.892742.509938.1328
81.7062-0.0371-1.69491.16480.10061.5040.1976-0.12950.3998-0.41640.0135-0.1964-0.31690.14-0.16720.7044-0.0437-0.01640.5884-0.02260.525785.858554.514917.8111
90.9809-0.8191-0.95821.22250.31431.9803-0.08230.1581-0.2583-0.1631-0.18350.09570.3108-0.25830.22990.6485-0.0799-0.03940.5867-0.06020.576173.18542.653919.2703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 35-62A35 - 62
2X-RAY DIFFRACTION2chain A and resid 63-91A63 - 91
3X-RAY DIFFRACTION3chain A and resid 108-144A108 - 144
4X-RAY DIFFRACTION4chain A and resid 145-164A145 - 164
5X-RAY DIFFRACTION5chain A and resid 203-242A203 - 242
6X-RAY DIFFRACTION6chain A and resid 263-291A263 - 291
7X-RAY DIFFRACTION7chain A and resid 307-346A307 - 346
8X-RAY DIFFRACTION8chain LL1 - 214
9X-RAY DIFFRACTION9chain HH1 - 217

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