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- PDB-2rh1: High resolution crystal structure of human B2-adrenergic G protei... -

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Basic information

Entry
Database: PDB / ID: 2rh1
TitleHigh resolution crystal structure of human B2-adrenergic G protein-coupled receptor.
Componentsbeta-2-adrenergic receptor/T4-lysozyme chimera
KeywordsMEMBRANE PROTEIN / HYDROLASE / GPCR / 7TM / adrenergic / fusion / lipidic cubic phase / lipidic / mesophase / cholesterol / membrane protein / MEMBRANE PROTEIN - HYDROLASE COMPLEX / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / GPCR Network
Function / homology
Function and homology information


desensitization of G protein-coupled receptor signaling pathway by arrestin / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / 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 ...desensitization of G protein-coupled receptor signaling pathway by arrestin / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / 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 / 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 / endosome to lysosome transport / adrenergic receptor signaling pathway / 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 / adenylate cyclase-activating adrenergic receptor signaling pathway / brown fat cell differentiation / regulation of sodium ion transport / bone resorption / viral release from host cell by cytolysis / activation of adenylate cyclase activity / receptor-mediated endocytosis / response to cold / peptidoglycan catabolic process / 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 / amyloid-beta binding / positive regulation of cold-induced thermogenesis / G alpha (s) signalling events / host cell cytoplasm / positive regulation of MAPK cascade / transcription by RNA polymerase II / lysosome / cell surface receptor signaling pathway / receptor complex / early endosome / 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 / membrane / identical protein binding / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / ACETAMIDE / 1,4-BUTANEDIOL / Chem-CAU / CHOLESTEROL / PALMITIC ACID / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsCherezov, V. / Rosenbaum, D.M. / Hanson, M.A. / Rasmussen, S.G.F. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Kuhn, P. / Weis, W.I. / Kobilka, B.K. ...Cherezov, V. / Rosenbaum, D.M. / Hanson, M.A. / Rasmussen, S.G.F. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Kuhn, P. / Weis, W.I. / Kobilka, B.K. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR)
Citation
Journal: Science / Year: 2007
Title: High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor.
Authors: Cherezov, V. / Rosenbaum, D.M. / Hanson, M.A. / Rasmussen, S.G. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Kuhn, P. / Weis, W.I. / Kobilka, B.K. / Stevens, R.C.
#1: Journal: To be Published
Title: GPCR Engineering Yields High-Resolution Structural Insights into beta2 Adrenergic Receptor Function.
Authors: Rosenbaum, D.M. / Cherezov, V. / Hanson, M.A. / Rasmussen, S.G.F. / Thian, F.S. / Kobilka, T.S. / Choi, H.J. / Yao, X.J. / Weis, W.I. / Stevens, R.C. / Kobilka, B.K.
History
DepositionOct 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 8, 2012Group: Other
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN THE PALMITIC ACID (PLM) AND ACETAMIDE (ACM) GROUPS ARE COVALENTLY LINKED TO THEIR ...HETEROGEN THE PALMITIC ACID (PLM) AND ACETAMIDE (ACM) GROUPS ARE COVALENTLY LINKED TO THEIR RESPECTIVE CYSTEINE RESIDUES.
Remark 999SEQUENCE THE STRUCTURE IS AN INTERNAL FUSION PROTEIN WITH LYSOZYME. AN OFFSET 1000 HAS BEEN ADDED ...SEQUENCE THE STRUCTURE IS AN INTERNAL FUSION PROTEIN WITH LYSOZYME. AN OFFSET 1000 HAS BEEN ADDED TO ORIGINAL SEQUENCE DATABASE RESIDUE NUMBERS (2-161) OF THE LYSOZYME PART IN COORDINATES TO DISTINGUISH THE LYSOZYME PART IN THE CHAIN. THEREFORE THE RESIDUES OF LYSOZYME PART HAVE NUMBERS A1002-A1161.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-2-adrenergic receptor/T4-lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,02117
Polymers56,6011
Non-polymers3,41916
Water86548
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.318, 169.240, 40.154
Angle α, β, γ (deg.)90.00, 105.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

DetailsAuthors state that the biological unit is unknown

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein beta-2-adrenergic receptor/T4-lysozyme chimera / Beta-2 adrenergic receptor / Beta-2 adrenoceptor / Beta-2 adrenoreceptor / Lysis protein / ...Beta-2 adrenergic receptor / Beta-2 adrenoceptor / Beta-2 adrenoreceptor / Lysis protein / Muramidase / Endolysin


Mass: 56601.438 Da / Num. of mol.: 1 / Mutation: N187E, C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Genus: Homo, T4-like viruses / Species: , Enterobacteria phage T4 sensu lato / Strain: ,
Description: The construct has been obtained by overlapping extension PCR
Gene: ADRB2, ADRB2R, B2AR / E / Plasmid: pFastbac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: P00720
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 8 types, 63 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CAU / (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol / (S)-Carazolol


Mass: 298.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O2
#5: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-ACM / ACETAMIDE / Acetamide


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#7: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#8: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#9: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 27

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.98 %
Description: This structure is a part of the Roadmap/PSI community outreach program, not a specific PSI target.
Crystal growTemperature: 293 K / Method: lipidic mesophase / pH: 6.75
Details: 30-35% v/v PEG 400, 0.1-0.2 M Na2SO4, 0.1 M Bis-tris propane pH 6.5-7.0, 5-7% 1,4-Butanediol, 8-10% Cholesterol, 52-50% Monoolein, pH 6.75, LIPIDIC MESOPHASE, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1781
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.03321
SYNCHROTRONAPS 23-ID-B21.03321
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDJun 22, 2007mirrors
MARMOSAIC 300 mm CCD2CCDJul 18, 2007mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 26705 / Num. obs: 26506 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.908 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.62
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.4-2.50.6782.2146723060199.1
2.5-2.60.5892.7141082558199.3
2.6-2.70.6024.1237722275199.9
2.7-2.80.4955197021893199.7
2.8-30.386.43315831301100
3-60.1331412600811968199.8
6-80.09920104801003199.6
8-100.07622.63591354199.4
10-200.06623.23352333187.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1U19, 2LZM

1u19

2lzm


Resolution: 2.4→19.95 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 18.501 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Water #548 has strong difference density but weak 2Fo-Fc density.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1310 4.9 %RANDOM
Rwork0.196 ---
all0.198 26506 --
obs0.198 26506 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å22.26 Å2
2---3.46 Å20 Å2
3---4.25 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3543 0 213 48 3804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223843
X-RAY DIFFRACTIONr_bond_other_d00.022622
X-RAY DIFFRACTIONr_angle_refined_deg1.525219
X-RAY DIFFRACTIONr_angle_other_deg4.0993.0026377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8765441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60423.182154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38315627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1641522
X-RAY DIFFRACTIONr_chiral_restr0.060.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.024008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02804
X-RAY DIFFRACTIONr_nbd_refined0.1870.3926
X-RAY DIFFRACTIONr_nbd_other0.1940.32443
X-RAY DIFFRACTIONr_nbtor_refined0.180.51935
X-RAY DIFFRACTIONr_nbtor_other0.1070.51580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.5194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.140.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.56
X-RAY DIFFRACTIONr_mcbond_it2.35222884
X-RAY DIFFRACTIONr_mcbond_other0.0972896
X-RAY DIFFRACTIONr_mcangle_it2.7672.53571
X-RAY DIFFRACTIONr_scbond_it4.58221974
X-RAY DIFFRACTIONr_scangle_it5.8492.51648
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 78 -
Rwork0.27 1829 -
all-1907 -
obs--98.76 %
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)
13.1220.86430.61462.6914-0.86325.9787-0.1453-0.22250.21160.0984-0.0656-0.0133-0.1849-0.17610.2109-0.22080.0432-0.0594-0.2598-0.0241-0.7033-23.68458.40530.485
29.6406-6.5961-0.980316.65013.28827.1133-0.1628-0.10080.4114-0.7585-0.10580.7355-0.659-0.60730.26860.04140.0577-0.1559-0.0871-0.0085-0.4908-35.05869.00111.961
32.3672.10680.85916.15510.78641.9314-0.03460.0267-0.2068-0.50090.07120.23880.32080.0002-0.0366-0.0103-0.0025-0.0974-0.2341-0.0034-0.5401-33.07420.0137.122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1002 - 1011238 - 247
2X-RAY DIFFRACTION1AA1062 - 1161298 - 397
3X-RAY DIFFRACTION2AA1012 - 1061248 - 297
4X-RAY DIFFRACTION3AA29 - 23036 - 237
5X-RAY DIFFRACTION3AA263 - 342398 - 477

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