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- PDB-2y03: TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND B... -

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Basic information

Entry
Database: PDB / ID: 2y03
TitleTURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND AGONIST ISOPRENALINE
ComponentsBETA-1 ADRENERGIC RECEPTOR
KeywordsRECEPTOR / G PROTEIN COUPLED RECEPTOR / SEVEN-HELIX RECEPTOR / INTEGRAL MEMBRANE PROTEIN / THERMOSTABILISING POINT MUTATIONS / GPCR / 7TM RECEPTOR
Function / homology
Function and homology information


beta1-adrenergic receptor activity / positive regulation of heart contraction / 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 / positive regulation of MAPK cascade / 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
ISOPRENALINE / CHOLESTEROL HEMISUCCINATE / Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMELEAGRIS GALLOPAVO (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWarne, A. / Moukhametzianov, R. / Baker, J.G. / Nehme, R. / Edwards, P.C. / Leslie, A.G.W. / Schertler, G.F.X. / Tate, C.G.
Citation
Journal: Nature / Year: 2011
Title: The Structural Basis for Agonist and Partial Agonist Action on a Beta1-Adrenergic Receptor
Authors: Warne, A. / Moukhametzianov, R. / Baker, J.G. / Nehme, R. / Edwards, P.C. / Leslie, A.G.W. / Schertler, G.F.X. / Tate, C.G.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Conformational Thermostabilization of the Beta1- Adrenergic Receptor in a Detergent-Resistant Form.
Authors: Serrano-Vega, M.J. / Magnani, F. / Shibata, Y. / Tate, C.G.
#2: Journal: Nature / Year: 2008
Title: Structure of a Beta1-Adrenergic G-Protein-Coupled Receptor.
Authors: Warne, T. / Serrano-Vega, M.J. / Baker, J.G. / Moukhametzianov, R. / Edwards, P.C. / Henderson, R. / Leslie, A.G.W. / Tate, C.G. / Schertler, G.F.X.
History
DepositionNov 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,57713
Polymers71,8822
Non-polymers3,69611
Water18010
1
A: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8007
Polymers35,9411
Non-polymers1,8596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7776
Polymers35,9411
Non-polymers1,8365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-32.2 kcal/mol
Surface area29950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.700, 61.600, 101.600
Angle α, β, γ (deg.)90.00, 109.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALA1AA47 - 6517 - 35
21LEULEUALAALA1BB47 - 6517 - 35
12LEULEUPHEPHE1AA75 - 9745 - 67
22LEULEUPHEPHE1BB75 - 9745 - 67
13SERSERILEILE1AA111 - 14381 - 113
23SERSERILEILE1BB111 - 14381 - 113
14METMETPROPRO1AA153 - 176123 - 146
24METMETPROPRO1BB153 - 176123 - 146
15ARGARGPROPRO1AA205 - 219175 - 189
25ARGARGPROPRO1BB205 - 219175 - 189
16ILEILEVALVAL1AA222 - 226192 - 196
26ILEILEVALVAL1BB222 - 226192 - 196
17ARGARGTRPTRP1AA279 - 303221 - 245
27ARGARGTRPTRP1BB279 - 303221 - 245
18LEULEUALAALA1AA331 - 358273 - 300
28LEULEUALAALA1BB331 - 358273 - 300
19ALAALALEULEU4AA33 - 463 - 16
29ALAALALEULEU4BB33 - 463 - 16
110GLYGLYGLYGLY4AA98 - 11068 - 80
210GLYGLYGLYGLY4BB98 - 11068 - 80

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35940.777 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-368 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 OF THE THIRD INTRACELLULAR LOOP WERE DELETED FROM THE CONSTRUCT. THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 367 AND A HEXAHIS TAG ADDED.
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

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Non-polymers , 5 types, 21 molecules

#2: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4
#3: Chemical
ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#4: Chemical ChemComp-5FW / ISOPRENALINE


Mass: 211.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO3 / Comment: medication*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

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
Has protein modificationY
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: 3.78 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: SITTING DROP VAPOUR DIFFUSION, PROTEIN (15MG/ML) IN 100MM NACL, 0.1MM EDTA, 1.0MM (R)-ISOPRENALINE, 0.45MG/ML CHS, 0.5% HEGA-10, 0.1M TRIS-HCL PH8.5, 28% PEG600 AT 4 DEGREES C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.85→42.25 Å / Num. obs: 24016 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 57.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7
Reflection shellResolution: 2.85→3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.8 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VT4

2vt4


Resolution: 2.85→95.69 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.904 / SU B: 13.006 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.778 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25353 1225 5.1 %RANDOM
Rwork0.21992 ---
obs0.22166 22791 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.376 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20.57 Å2
2---0.08 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.85→95.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4659 0 193 10 4862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224967
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9876751
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46621.955179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.73615813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.941536
X-RAY DIFFRACTIONr_chiral_restr0.0970.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213520
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_it1.59532928
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.12154750
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.05852039
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.626102001
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1327tight positional0.050.05
2B1327tight positional0.050.05
1A208medium positional0.060.5
2B208medium positional0.060.5
1A1327tight thermal3.6810
2B1327tight thermal3.6810
1A208medium thermal3.7220
2B208medium thermal3.7220
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 83 -
Rwork0.286 1684 -
obs--96.72 %

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