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

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Basic information

Entry
Database: PDB / ID: 2ycz
TitleTURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND ANTAGONIST IODOCYANOPINDOLOL
ComponentsBETA-1 ADRENERGIC RECEPTOR
KeywordsRECEPTOR / GPCR / TRANSDUCER / ANTAGONIST BOUND FORM / INTEGRAL MEMBRANE PROTEIN / G-PROTEIN COUPLED RECEPTOR / THERMOSTABILISING POINT MUTATIONS / SEVEN-HELIX RECEPTOR / 7TM RECEPTOR
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
Chem-I32 / Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMELEAGRIS GALLOPAVO (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsMoukhametzianov, R. / Warne, T. / Edwards, P.C. / Serrano-Vega, M.J. / Leslie, A.G.W. / Tate, C.G. / Schertler, G.F.X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Two Distinct Conformations of Helix 6 Observed in Antagonist-Bound Structures of a {Beta}1- Adrenergic Receptor.
Authors: Moukhametzianov, R. / Warne, T. / Edwards, P.C. / Serrano-Vega, M.J. / Leslie, A.G. / Tate, C.G. / Schertler, G.F.
History
DepositionMar 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 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)72,6405
Polymers71,5052
Non-polymers1,1353
Water00
1
A: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1662
Polymers35,7531
Non-polymers4131
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-1 ADRENERGIC RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4743
Polymers35,7531
Non-polymers7222
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.855, 56.298, 110.939
Angle α, β, γ (deg.)90.00, 116.39, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A39 - 240
2111B39 - 240
1211A257 - 329
2211B257 - 329

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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: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 AND 277-278 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
#2: Chemical ChemComp-I32 / 4-{[(2S)-3-(tert-butylamino)-2-hydroxypropyl]oxy}-3-iodo-1H-indole-2-carbonitrile / IODOCYANOPINDOLOL


Mass: 413.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20IN3O2 / Comment: antagonist*YM
#3: Sugar ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM
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: 3.48 Å3/Da / Density % sol: 64.64 %
Description: DATA WERE COLLECTED IN WEDGES BY SCANNING FROM MULTIPLE SPOTS ON THE CRYSTAL
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.65→41.3 Å / Num. obs: 11215 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 71.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.6
Reflection shellResolution: 3.65→3.71 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VT4

2vt4


Resolution: 3.65→41.31 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.833 / SU B: 32.783 / SU ML: 0.502 / Cross valid method: THROUGHOUT / ESU R Free: 0.667 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27046 536 4.8 %RANDOM
Rwork0.24903 ---
obs0.25005 10678 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-2.58 Å2
2---6.82 Å20 Å2
3---3.67 Å2
Refinement stepCycle: LAST / Resolution: 3.65→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 64 0 4712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224830
X-RAY DIFFRACTIONr_bond_other_d0.0070.023260
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.9696579
X-RAY DIFFRACTIONr_angle_other_deg0.8643.0027846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5415580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.26821.667180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6615816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.0081538
X-RAY DIFFRACTIONr_chiral_restr0.050.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025158
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021056
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_it3.561.52906
X-RAY DIFFRACTIONr_mcbond_other1.3371.51164
X-RAY DIFFRACTIONr_mcangle_it6.27824722
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.1331924
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.0964.51857
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: 3674 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
1Atight thermal1.110.5
2Btight thermal1.110.5
LS refinement shellResolution: 3.65→3.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 37 -
Rwork0.287 808 -
obs--100 %

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