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- PDB-4ami: Turkey beta1 adrenergic receptor with stabilising mutations and b... -

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Basic information

Entry
Database: PDB / ID: 4ami
TitleTurkey beta1 adrenergic receptor with stabilising mutations and bound biased agonist bucindolol
ComponentsBETA-1 ADRENERGIC RECEPTOR
KeywordsMEMBRANE PROTEIN / 7TMR BETA1-ADRENOCEPTOR / STABILISING MUTATIONS / BIASED AGONIST
Function / homology
Function and homology information


beta1-adrenergic receptor activity / positive regulation of heart contraction / regulation of circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of GTPase activity / early endosome / membrane / identical protein binding / 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
Chem-G90 / Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMELEAGRIS GALLOPAVO (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWarne, T. / Edwards, P.C. / Leslie, A.G. / Tate, C.G.
CitationJournal: Structure / Year: 2012
Title: Crystal Structures of a Stabilized Beta1-Adrenoceptor Bound to the Biased Agonists Bucindolol and Carvedilol
Authors: Warne, T. / Edwards, P.C. / Leslie, A.G. / Tate, C.G.
History
DepositionMar 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Other
Revision 1.2Dec 3, 2014Group: Derived calculations
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: BETA-1 ADRENERGIC RECEPTOR
B: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5069
Polymers71,8822
Non-polymers2,6247
Water23413
1
A: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6843
Polymers35,9411
Non-polymers7432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8226
Polymers35,9411
Non-polymers1,8815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.844, 60.677, 107.818
Angle α, β, γ (deg.)90.00, 110.78, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B47 - 103
2111A47 - 103
1211B113 - 140
2211A113 - 140
1311B153 - 170
2311A153 - 170
1411B176 - 182
2411A176 - 182
1511B202 - 230
2511A202 - 230
1611B291 - 311
2611A291 - 311
1711B329 - 358
2711A329 - 358

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999443, 0.033183, 0.003584), (0.029228, 0.818309, 0.574035), (0.016115, 0.57382, -0.818823)-15.10151, -15.0103, 48.81022

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Components

#1: Protein BETA-1 ADRENERGIC RECEPTOR / / BETA-1 ADRENORECEPTOR / BETA-1 ADRENOCEPTOR / BETA-T


Mass: 35940.777 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-243,272-368 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MELEAGRIS GALLOPAVO (turkey) / Cell: ERYTHROCYTE / Plasmid: PBACPAK8 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P07700
#2: Chemical ChemComp-G90 / 2-[(2S)-3-[[1-(1H-indol-3-yl)-2-methyl-propan-2-yl]amino]-2-oxidanyl-propoxy]benzenecarbonitrile / BUCINDOLOL / Bucindolol


Mass: 363.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N3O2
#3: Chemical
ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 68 TO SER ENGINEERED RESIDUE IN CHAIN A, MET 90 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, ARG 68 TO SER ENGINEERED RESIDUE IN CHAIN A, MET 90 TO VAL ENGINEERED RESIDUE IN CHAIN A, CYS 116 TO LEU ENGINEERED RESIDUE IN CHAIN A, TYR 227 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 282 TO LEU ENGINEERED RESIDUE IN CHAIN A, PHE 327 TO ALA ENGINEERED RESIDUE IN CHAIN A, PHE 338 TO MET ENGINEERED RESIDUE IN CHAIN A, CYS 358 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 68 TO SER ENGINEERED RESIDUE IN CHAIN B, MET 90 TO VAL ENGINEERED RESIDUE IN CHAIN B, CYS 116 TO LEU ENGINEERED RESIDUE IN CHAIN B, TYR 227 TO ALA ENGINEERED RESIDUE IN CHAIN B, ALA 282 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 327 TO ALA ENGINEERED RESIDUE IN CHAIN B, PHE 338 TO MET ENGINEERED RESIDUE IN CHAIN B, CYS 358 TO ALA
Sequence detailsTHE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY R68S,M90V,Y227A,A282L,F327A,F338M THE ...THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY R68S,M90V,Y227A,A282L,F327A,F338M THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE EXPRESSION AND HELP CRYSTALLISATION C116L, C358A

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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: 3.82 Å3/Da / Density % sol: 67.8 % / Description: NONE
Crystal growTemperature: 277 K / pH: 9
Details: 0.1 M BICINE PH 9.0, 22% PEG 600, 4 DEGREES CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→52.1 Å / Num. obs: 17466 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 86.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y02

2y02


Resolution: 3.2→44.82 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.844 / SU B: 19.89 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27892 898 5.1 %RANDOM
Rwork0.24236 ---
obs0.24421 16557 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.661 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.88 Å2
2--3.34 Å20 Å2
3----2.55 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 131 13 4673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024771
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9841.9776486
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2385566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45522.184174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57515781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.61532
X-RAY DIFFRACTIONr_chiral_restr0.0670.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213419
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1469 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Rms dev position: 4.8 Å / Weight position: 0.5

Dom-IDAuth asym-ID
2A
1B
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 55 -
Rwork0.35 1091 -
obs--86.69 %

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