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- PDB-7bts: Structure of human beta1 adrenergic receptor bound to epinephrine... -

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Basic information

Entry
Database: PDB / ID: 7bts
TitleStructure of human beta1 adrenergic receptor bound to epinephrine and nanobody 6B9
Components
  • Camelid Antibody Fragment
  • Lysozyme-Beta-1 adrenergic receptor chimera
KeywordsMEMBRANE PROTEIN / G protein coupled receptor
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) / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate / L-EPINEPHRINE / CHOLESTEROL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 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 2, 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: Lysozyme-Beta-1 adrenergic receptor chimera
B: Camelid Antibody Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,89313
Polymers65,1852
Non-polymers1,70811
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-87 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)377.980, 66.220, 47.860
Angle α, β, γ (deg.)90.000, 93.883, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Lysozyme-Beta-1 adrenergic receptor chimera / Lysis protein / Lysozyme / Muramidase


Mass: 52235.879 Da / Num. of mol.: 1 / Mutation: C944T,C987A
Source method: isolated from a genetically manipulated source
Details: Chain A 1261 Cys to Chain A 1314 LEU are truncated region.
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126, ADRB1, ADRB1R, B1AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D9IEF7, lysozyme
#2: Antibody Camelid Antibody Fragment


Mass: 12949.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Spodoptera frugiperda (fall armyworm)

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Non-polymers , 6 types, 11 molecules

#3: Chemical ChemComp-ALE / L-EPINEPHRINE / ADRENALINE


Mass: 183.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#8: Chemical ChemComp-1WV / (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate


Mass: 300.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32O4

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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 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: 4.59 Å3/Da / Density % sol: 73.2 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM HEPES, pH 7.5, 80-180 mM Sodium Sulfate, 38-42% PEG400 or PEG300, 10mM epinephrine

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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: Feb 4, 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: 3.1→50 Å / Num. obs: 20331 / % possible obs: 96.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 74.88 Å2 / CC1/2: 0.982 / Net I/σ(I): 5.59
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 897 / CC1/2: 0.5 / % possible all: 58.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LDE

4lde


Resolution: 3.13→19.98 Å / SU ML: 0.429 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2585 1705 8.39 %
Rwork0.2355 18626 -
obs0.2374 20331 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.32 Å2
Refinement stepCycle: LAST / Resolution: 3.13→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 102 0 4526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01524617
X-RAY DIFFRACTIONf_angle_d0.78346282
X-RAY DIFFRACTIONf_chiral_restr0.1922717
X-RAY DIFFRACTIONf_plane_restr0.0037774
X-RAY DIFFRACTIONf_dihedral_angle_d20.8886649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13-3.220.3897920.3372975X-RAY DIFFRACTION62.29
3.22-3.330.32741490.31831572X-RAY DIFFRACTION99.65
3.33-3.450.33181500.30871604X-RAY DIFFRACTION100
3.45-3.580.34331460.25791565X-RAY DIFFRACTION100
3.58-3.740.27181410.25541624X-RAY DIFFRACTION99.94
3.75-3.940.26351530.24961579X-RAY DIFFRACTION100
3.94-4.190.27341570.2391573X-RAY DIFFRACTION100
4.19-4.510.26911490.2231611X-RAY DIFFRACTION100
4.51-4.950.24681510.22191579X-RAY DIFFRACTION100
4.95-5.650.23351350.24021634X-RAY DIFFRACTION100
5.66-7.070.25911430.24061630X-RAY DIFFRACTION100
7.07-19.980.17061390.17661680X-RAY DIFFRACTION99.78

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