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- PDB-7bvq: Structure of human beta1 adrenergic receptor bound to carazolol -

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Basic information

Entry
Database: PDB / ID: 7bvq
TitleStructure of human beta1 adrenergic receptor bound to carazolol
ComponentsEndolysin,Beta-1 adrenergic receptor chimera
KeywordsMEMBRANE PROTEIN / G protein coupled receptor / SIGNALING PROTEIN
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme ...Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate / Chem-CAU / CITRIC ACID / CHOLESTEROL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXu, X. / Kaindl, J. / Clark, M. / Hubner, H. / Hirata, K. / Sunahara, R. / Gmeiner, P. / Kobilka, B.K. / Liu, X.
CitationJournal: Cell Res. / Year: 2021
Title: Binding pathway determines norepinephrine selectivity for the human beta 1 AR over beta 2 AR.
Authors: Xu, X. / Kaindl, J. / Clark, M.J. / Hubner, H. / Hirata, K. / Sunahara, R.K. / Gmeiner, P. / Kobilka, B.K. / Liu, X.
History
DepositionApr 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 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: Endolysin,Beta-1 adrenergic receptor chimera
B: Endolysin,Beta-1 adrenergic receptor chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,35123
Polymers104,4722
Non-polymers3,87921
Water2,180121
1
A: Endolysin,Beta-1 adrenergic receptor chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,78816
Polymers52,2361
Non-polymers2,55215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin,Beta-1 adrenergic receptor chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5637
Polymers52,2361
Non-polymers1,3276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.134, 52.825, 142.749
Angle α, β, γ (deg.)92.137, 90.714, 116.647
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Endolysin,Beta-1 adrenergic receptor chimera / Lysozyme / Muramidase


Mass: 52235.879 Da / Num. of mol.: 2 / Mutation: C944T,C987A
Source method: isolated from a genetically manipulated source
Details: 1261 Cys to 1314 LEU are truncated region.,1261 Cys to 1314 LEU are truncated region.
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D9IEF7, lysozyme
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 8 types, 141 molecules

#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-CAU / (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol / (S)-Carazolol


Mass: 298.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-1WV / (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate


Mass: 300.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C17H32O4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#9: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
Sequence detailsTHE GENEBANK ENTRY NP_000675 IS A REFERENCE SEQUENCE FOR THE RESIDUES FROM 171TH TO 462TH OF OF CHAIN A.

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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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Sodium citrate, pH 5, 150-170 mM lithium sulfate, 38-42% PEG300, 3% 1,3-butanediol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 9, 2018
RadiationMonochromator: liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 46879 / % possible obs: 99.7 % / Redundancy: 33.3 % / Biso Wilson estimate: 46.84 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.01
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 5182 / CC1/2: 0.486

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rh1

2rh1


Resolution: 2.5→19.79 Å / SU ML: 0.3512 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 26.4209
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2633 2418 5.16 %
Rwork0.225 44434 -
obs0.2269 46852 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.69 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7012 0 244 121 7377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817400
X-RAY DIFFRACTIONf_angle_d0.819210060
X-RAY DIFFRACTIONf_chiral_restr0.23171168
X-RAY DIFFRACTIONf_plane_restr0.00531227
X-RAY DIFFRACTIONf_dihedral_angle_d22.30421047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.33421500.30672559X-RAY DIFFRACTION99.6
2.55-2.610.33151290.28752651X-RAY DIFFRACTION99.57
2.61-2.670.28911330.27542580X-RAY DIFFRACTION99.93
2.67-2.730.28831520.26172639X-RAY DIFFRACTION99.82
2.73-2.810.29241490.2452583X-RAY DIFFRACTION99.74
2.81-2.890.29561690.24562627X-RAY DIFFRACTION99.75
2.89-2.980.25891650.24742543X-RAY DIFFRACTION99.89
2.98-3.090.291750.23712639X-RAY DIFFRACTION99.96
3.09-3.210.23891310.23192575X-RAY DIFFRACTION99.89
3.21-3.360.30141160.22742650X-RAY DIFFRACTION100
3.36-3.530.24221050.22432662X-RAY DIFFRACTION99.86
3.53-3.750.26191480.2122642X-RAY DIFFRACTION100
3.75-4.040.25161520.21332610X-RAY DIFFRACTION99.96
4.04-4.440.25221340.20732608X-RAY DIFFRACTION100
4.44-5.080.2789870.21942666X-RAY DIFFRACTION100
5.08-6.360.28871370.25132621X-RAY DIFFRACTION100
6.36-19.790.21431860.18132579X-RAY DIFFRACTION99.78

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