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- PDB-4gpo: Oligomeic Turkey Beta1-Adrenergic G Protein-Coupled Receptor -

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Basic information

Entry
Database: PDB / ID: 4gpo
TitleOligomeic Turkey Beta1-Adrenergic G Protein-Coupled Receptor
ComponentsBeta-1 adrenergic receptor
KeywordsRECEPTOR / seven-transmembrane helix receptor / G-protein coupled receptor
Function / homology
Function and homology information


beta1-adrenergic receptor activity / positive regulation of heart rate by epinephrine-norepinephrine / regulation of circadian sleep/wake cycle, sleep / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-activating adrenergic receptor signaling pathway / early endosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Beta 1 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 1 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHuang, J.J. / Chen, S. / Zhang, J.J. / Huang, X.Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Crystal structure of oligomeric beta-1-adrenergic G protein-coupled receptors in ligand-free basal state.
Authors: Huang, J. / Chen, S. / Zhang, J.J. / Huang, X.Y.
History
DepositionAug 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Refinement description
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-1 adrenergic receptor
B: Beta-1 adrenergic receptor


Theoretical massNumber of molelcules
Total (without water)71,5052
Polymers71,5052
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-14 kcal/mol
Surface area30210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.660, 79.590, 69.040
Angle α, β, γ (deg.)90.00, 101.83, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 36:237 or resseq 280:356 )
211chain B and (resseq 36:237 or resseq 280:356 )

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Components

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


Mass: 35752.598 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-243,272-276,279-367 / Mutation: STABILISING MUTATIONS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / Gene: ADRB1 / Plasmid: pVL1393 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: P07700

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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: 4.32 Å3/Da / Density % sol: 71.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20mM sodium acetate, 100-300mM ammonium sulfate, 26~30% PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 291K
PH range: 3.6-4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.35→67.57 Å / Num. obs: 17463 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 6.3
Reflection shellResolution: 3.35→3.44 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 1275 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y04

2y04


Resolution: 3.5→29.779 Å / SU ML: 1.54 / σ(F): 1.99 / Phase error: 40.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3546 642 4.94 %RANDOM
Rwork0.3099 ---
obs0.3121 13006 83.62 %-
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.906 Å2 / ksol: 0.254 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4683 Å2-0 Å212.3701 Å2
2--3.7643 Å20 Å2
3----9.5631 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 0 0 4442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064554
X-RAY DIFFRACTIONf_angle_d1.1366205
X-RAY DIFFRACTIONf_dihedral_angle_d17.261593
X-RAY DIFFRACTIONf_chiral_restr0.084746
X-RAY DIFFRACTIONf_plane_restr0.005745
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2217X-RAY DIFFRACTIONPOSITIONAL
12B2217X-RAY DIFFRACTIONPOSITIONAL0.02
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.76980.5524730.47671428X-RAY DIFFRACTION48
3.7698-4.14830.47541000.36922160X-RAY DIFFRACTION74
4.1483-4.74640.32231520.26672881X-RAY DIFFRACTION98
4.7464-5.97210.34911400.29492931X-RAY DIFFRACTION99
5.9721-29.78040.29711770.29282964X-RAY DIFFRACTION98
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)
10.7954-0.39590.17260.7802-0.52261.0011-0.02310.1115-0.1781-0.2534-0.13290.1042-0.03910.1053-0.07550.2712-0.06870.0922-0.2136-0.08560.3455-32.0337-0.037310.0043
21.11220.2447-0.26880.4606-0.07980.8440.3702-0.5973-0.3338-0.2171-0.04320.48350.06160.71480.7066-0.7398-0.19370.6566-0.3670.3722-0.8309-31.677914.850415.6039
30.0327-0.0144-0.06770.00520.04270.13510.0179-0.0971-0.05460.00050.0745-0.0461-0.0430.16930.06830.4548-0.1557-0.36520.9595-0.2423-0.0206-13.817229.091429.0225
40.58390.1082-0.10970.7618-0.30280.9321-0.0763-0.3164-0.1530.08640.19180.4947-0.39150.34690.01980.1652-0.0030.098-0.42420.2858-0.1209-40.846524.35726.5952
50.558-0.12840.62640.3792-0.5971.3548-0.2215-0.03020.4020.0832-0.08-0.15-0.1820.2668-0.21970.4419-0.4605-0.12320.1795-0.22580.2844-9.630226.828813.3294
63.0940.31770.8891.55310.29182.1557-0.0385-0.05830.0589-0.3286-0.03660.0436-0.1503-0.05950.09940.39270.0648-0.91640.5006-0.01960.8922-19.869118.57617.0111
72.2998-0.60091.01690.1917-0.55713.0273-0.03590.70490.2198-0.3927-0.05470.317-0.0078-0.11480.00560.71050.2702-0.80070.46270.06830.5676-33.082314.4248-5.7092
81.7356-0.52470.54741.7364-2.14762.6998-0.2679-0.5086-0.15970.1584-0.0303-0.23840.06430.4482-0.21930.29190.1552-0.10980.3679-0.3360.5314-18.16936.035719.5227
90.93660.6383-0.41170.56190.03290.9693-0.0043-0.1785-0.0662-0.2307-0.10290.0969-0.32630.20610.03350.55340.0796-0.14170.08830.03950.6228-35.32-8.45413.858
100.7269-0.09420.02530.7476-0.68751.7315-0.3173-0.19390.07860.2771-0.3312-0.42780.10360.6493-0.45150.0425-0.31620.16920.110.3032-0.1007-19.5419-22.28219.8999
111.83781.5638-0.79851.47860.15435.1686-0.00630.11490.3276-0.16710.15160.3846-0.5482-0.3470.02480.3690.072-0.3093-0.06820.16810.5556-40.9625-14.6983.192
120.9418-0.3460.14340.3565-0.07970.95090.0649-0.23480.07220.1962-0.14740.10260.05440.0496-0.2642-0.65360.45660.4497-0.2127-0.228-0.1099-31.2626-29.11513.6133
13-0.00560.002-0.0009-0.00220.00120.001-0.14710.1479-0.2235-0.24850.22910.05730.00450.1279-0.03450.68410.2191-0.3271.5539-0.27211.3272-13.2429-37.47728.4213
142.27790.11250.74431.11870.19931.2305-0.30480.06280.2196-0.360.05280.2668-0.33390.1133-0.0928-0.29090.1576-0.5946-0.00170.07670.0583-40.0747-32.8615.7378
153.08741.34790.20650.5860.09630.01510.4125-0.8612-0.38040.4597-0.268-0.31460.20610.1057-0.08550.4870.1436-0.34690.42450.0340.6947-27.7842-35.15535.823
162.0875-1.84721.42591.6583-1.36614.9132-0.1155-0.36260.19480.6684-0.0315-0.8926-0.26160.51660.12390.76420.1095-0.4950.5732-0.04020.8475-28.0644-24.73932.3494
172.2913-0.11931.23941.7004-0.03521.6306-0.05660.11590.0459-0.2312-0.15150.1726-0.1383-0.5088-0.08610.0525-0.0008-0.8840.63770.28971.0108-50.9389-28.65216.7077
180.6072-0.6399-0.36513.1116-0.09170.6221-0.007-0.06920.01060.02810.1036-0.12410.1140.07180.0480.40540.2491-0.74910.2215-0.11031.0227-36.3107-18.46920.7451
194.02733.5373-0.32298.37580.29142.574-0.111-0.1624-0.24550.13160.06520.45470.1678-0.4567-0.00791.0827-0.3367-0.07071.5914-0.20591.1822-16.1263-11.40727.9748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 35:66)A35 - 66
2X-RAY DIFFRACTION2chain 'A' and (resseq 67:140)A67 - 140
3X-RAY DIFFRACTION3chain 'A' and (resseq 141:157)A141 - 157
4X-RAY DIFFRACTION4chain 'A' and (resseq 158:217)A158 - 217
5X-RAY DIFFRACTION5chain 'A' and (resseq 218:282)A218 - 282
6X-RAY DIFFRACTION6chain 'A' and (resseq 283:315)A283 - 315
7X-RAY DIFFRACTION7chain 'A' and (resseq 316:332)A316 - 332
8X-RAY DIFFRACTION8chain 'A' and (resseq 333:356)A333 - 356
9X-RAY DIFFRACTION9chain 'B' and (resseq 35:66)B35 - 66
10X-RAY DIFFRACTION10chain 'B' and (resseq 67:92)B67 - 92
11X-RAY DIFFRACTION11chain 'B' and (resseq 93:110)B93 - 110
12X-RAY DIFFRACTION12chain 'B' and (resseq 111:140)B111 - 140
13X-RAY DIFFRACTION13chain 'B' and (resseq 141:157)B141 - 157
14X-RAY DIFFRACTION14chain 'B' and (resseq 158:217)B158 - 217
15X-RAY DIFFRACTION15chain 'B' and (resseq 218:282)B218 - 282
16X-RAY DIFFRACTION16chain 'B' and (resseq 283:302)B283 - 302
17X-RAY DIFFRACTION17chain 'B' and (resseq 303:323)B303 - 323
18X-RAY DIFFRACTION18chain 'B' and (resseq 324:345)B324 - 345
19X-RAY DIFFRACTION19chain 'B' and (resseq 346:356)B346 - 356

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