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- PDB-5a8e: thermostabilised beta1-adrenoceptor with rationally designed inve... -

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Basic information

Entry
Database: PDB / ID: 5a8e
Titlethermostabilised beta1-adrenoceptor with rationally designed inverse agonist 7-methylcyanopindolol bound
ComponentsBETA1 ADRENERGIC RECEPTOR
KeywordsSIGNALING PROTEIN / INVERSE 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 / 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
(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-XTK / Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMELEAGRIS GALLOPAVO (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsSato, T. / Baker, J.G. / Warne, T. / Brown, G.A. / Congreve, M. / Leslie, A.G.W. / Tate, C.G.
CitationJournal: Mol.Pharmacol. / Year: 2015
Title: Pharmacological Analysis and Structure Determination of 7-Methylcyanopindolol-Bound Beta1-Adrenergic Receptor.
Authors: Sato, T. / Baker, J. / Warne, T. / Brown, G. / Leslie, A. / Congreve, M. / Tate, C.
History
DepositionJul 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Jan 10, 2024Group: 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: BETA1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,25410
Polymers35,9341
Non-polymers2,3209
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.019, 61.777, 95.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BETA1 ADRENERGIC RECEPTOR


Mass: 35933.828 Da / Num. of mol.: 1 / 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, 35 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-XTK / 4-[(2S)-3-(tert-butylamino)-2-hydroxypropoxy]-7-methyl-1H-indole-2-carbonitrile


Mass: 301.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N3O2
#4: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY ...THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE THERMOSTABILITY R68S,M90V,I129V,Y227A,A282L,F327A,F338M, Y343L. THE FOLLOWING MUTATIONS WERE MADE TO IMPROVE EXPRESSION AND HELP CRYSTALLIZATION C116L, E130W,C358A.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.4 % / Description: NONE
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 25% PEG600, 0.1M ADA PH7.0, LIPIDIC CUBIC PHASE (LCP), TEMPERATURE 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID2910.8726
SYNCHROTRONDiamond I2420.969
Detector
TypeIDDetector
PILATUS1PIXEL
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.87261
20.9691
ReflectionResolution: 2.4→37.8 Å / Num. obs: 12526 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.9 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 4BVN

4bvn


Resolution: 2.4→37.79 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.905 / SU B: 9.816 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.561 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 608 4.8 %RANDOM
Rwork0.21683 ---
obs0.21835 11942 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.347 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 137 26 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022461
X-RAY DIFFRACTIONr_bond_other_d0.0020.022510
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9963323
X-RAY DIFFRACTIONr_angle_other_deg0.92135740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9875285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95121.8686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65415396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.621517
X-RAY DIFFRACTIONr_chiral_restr0.0640.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
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_it1.373.7121140
X-RAY DIFFRACTIONr_mcbond_other1.373.711139
X-RAY DIFFRACTIONr_mcangle_it2.3785.5551422
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5554.1061318
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
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 54 -
Rwork0.294 847 -
obs--98.04 %

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