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- PDB-7bu7: Structure of human beta1 adrenergic receptor bound to BI-167107 a... -

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Basic information

Entry
Database: PDB / ID: 7bu7
TitleStructure of human beta1 adrenergic receptor bound to BI-167107 and nanobody 6B9
Components
  • Endolysin,Endolysin,Beta-1 adrenergic receptor chimera
  • camelid antibody fragment
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
alpha-maltose / (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate / CHOLESTEROL / Chem-P0G / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
Camelidae mixed library (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 4, 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 1.3Nov 20, 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,Endolysin,Beta-1 adrenergic receptor chimera
B: camelid antibody fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,50816
Polymers71,6462
Non-polymers2,86214
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-90 kcal/mol
Surface area28060 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 / Sugars , 3 types, 4 molecules AB

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


Mass: 57625.109 Da / Num. of mol.: 1 / Mutation: C944T,C987A
Source method: isolated from a genetically manipulated source
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: 14020.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae mixed library (mammal)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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, 37 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#6: 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
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: 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
#9: Chemical ChemComp-P0G / 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one


Mass: 370.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N2O4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H26O7 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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 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: 4.51 Å3/Da / Density % sol: 72.73 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100mM HEPES, pH 7.5, 100-175mM (NH4)2SO4, 38-43% PEG400, 0.15M-0.2M Glycine

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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: 2.6→50 Å / Num. obs: 35466 / % possible obs: 96.7 % / Redundancy: 6.64 % / Biso Wilson estimate: 65.99 Å2 / CC1/2: 0.991 / Net I/σ(I): 4.66
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3325 / CC1/2: 0.451 / % possible all: 85

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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: 4lde

4lde


Resolution: 2.6→19.98 Å / SU ML: 0.3931 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.5599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2698 1994 5.66 %
Rwork0.2435 33265 -
obs0.245 35259 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.32 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4463 0 181 25 4669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01654738
X-RAY DIFFRACTIONf_angle_d1.19086435
X-RAY DIFFRACTIONf_chiral_restr0.2077734
X-RAY DIFFRACTIONf_plane_restr0.0038781
X-RAY DIFFRACTIONf_dihedral_angle_d17.786666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.33461200.30622097X-RAY DIFFRACTION83.88
2.67-2.740.36471380.32672097X-RAY DIFFRACTION88.1
2.74-2.820.36091300.32972291X-RAY DIFFRACTION90.91
2.82-2.910.35551420.31742255X-RAY DIFFRACTION93.78
2.91-3.010.3161390.30822383X-RAY DIFFRACTION96.52
3.01-3.130.32181420.28692406X-RAY DIFFRACTION98.91
3.13-3.270.30251420.28552427X-RAY DIFFRACTION99.38
3.27-3.450.2941530.26172450X-RAY DIFFRACTION99.54
3.45-3.660.25311510.24552444X-RAY DIFFRACTION99.85
3.66-3.940.28651530.2252451X-RAY DIFFRACTION99.73
3.94-4.330.22711440.22182482X-RAY DIFFRACTION99.92
4.33-4.950.26251470.22422438X-RAY DIFFRACTION99.58
4.95-6.20.28611440.252498X-RAY DIFFRACTION99.55
6.21-19.980.21471490.20072546X-RAY DIFFRACTION99.34

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