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- PDB-4lde: Structure of beta2 adrenoceptor bound to BI167107 and an engineer... -

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Basic information

Entry
Database: PDB / ID: 4lde
TitleStructure of beta2 adrenoceptor bound to BI167107 and an engineered nanobody
Components
  • Camelid Antibody Fragment
  • Lysozyme, Beta-2 adrenergic receptor
KeywordsMEMBRANE PROTEIN/HYDROLASE / G protein coupled receptor / MEMBRANE PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


: / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure ...: / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / response to psychosocial stress / negative regulation of multicellular organism growth / adrenergic receptor signaling pathway / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / adenylate cyclase binding / smooth muscle contraction / potassium channel regulator activity / positive regulation of bone mineralization / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / viral release from host cell by cytolysis / bone resorption / activation of adenylate cyclase activity / response to cold / peptidoglycan catabolic process / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein serine/threonine kinase activity / cellular response to amyloid-beta / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / Clathrin-mediated endocytosis / lysozyme activity / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / cell surface receptor signaling pathway / lysosome / early endosome / receptor complex / endosome membrane / Ub-specific processing proteases / endosome / defense response to bacterium / apical plasma membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme ...Beta 2 adrenoceptor / Adrenoceptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / 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) / Lysozyme-like domain superfamily / 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 / Chem-P0G / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsRing, A.M. / Manglik, A. / Kruse, A.C. / Enos, M.D. / Weis, W.I. / Garcia, K.C. / Kobilka, B.K.
CitationJournal: Nature / Year: 2013
Title: Adrenaline-activated structure of beta 2-adrenoceptor stabilized by an engineered nanobody.
Authors: Ring, A.M. / Manglik, A. / Kruse, A.C. / Enos, M.D. / Weis, W.I. / Garcia, K.C. / Kobilka, B.K.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme, Beta-2 adrenergic receptor
B: Camelid Antibody Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1145
Polymers66,4202
Non-polymers6943
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-18 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.670, 66.480, 303.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Lysozyme, Beta-2 adrenergic receptor / Endolysin / Lysis protein / Muramidase / Beta-2 adrenoreceptor / Beta-2 adrenoceptor


Mass: 53471.039 Da / Num. of mol.: 1
Fragment: UNP residues 29-348 with a deletion of residues 235-263
Mutation: C918T, C962A, M1096T, M1098T, N1157E, C1265A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: ADRB2, E, ADRB2R, B2AR / Plasmid: pVL1392 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00720, UniProt: P07550, lysozyme
#2: Antibody Camelid Antibody Fragment


Mass: 12949.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Engineered fragment / Source: (gene. exp.) Lama glama (llama) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 4 types, 87 molecules

#3: 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
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: 100 mM MES pH 6.2-6.7, 40-100 mM ammonium phosphate dibasic, 18-24% PEG400, LIPIDIC CUBIC PHASE, temperature 293K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.79→38.4 Å / Num. obs: 25028 / % possible obs: 95.8 % / Observed criterion σ(F): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 4.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1953 / % possible all: 81.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1241)refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P0G

3p0g


Resolution: 2.79→38.4 Å / SU ML: 0.43 / σ(F): 1.49 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 1255 5.01 %RANDOM
Rwork0.2269 ---
obs0.2284 25028 95.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 43 84 4614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054643
X-RAY DIFFRACTIONf_angle_d0.7256298
X-RAY DIFFRACTIONf_dihedral_angle_d12.2191624
X-RAY DIFFRACTIONf_chiral_restr0.052723
X-RAY DIFFRACTIONf_plane_restr0.003783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.89740.41261130.3682125X-RAY DIFFRACTION79
2.8974-3.02920.30741300.31582483X-RAY DIFFRACTION93
3.0292-3.18880.30851410.28532680X-RAY DIFFRACTION98
3.1888-3.38850.27781420.26222669X-RAY DIFFRACTION98
3.3885-3.64990.29461420.23982701X-RAY DIFFRACTION99
3.6499-4.01690.23961430.20522720X-RAY DIFFRACTION99
4.0169-4.59730.22231470.18442745X-RAY DIFFRACTION99
4.5973-5.7890.22661440.20692740X-RAY DIFFRACTION98
5.789-38.42380.23341530.20712910X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.58454.17140.98585.16560.56882.21860.10560.1973-0.14770.36080.05590.05380.16060.1057-0.13940.40180.0312-0.00440.2411-0.01440.4333-16.0036-29.6026-77.6145
22.43860.36460.04471.5743-1.03393.82380.0209-0.35380.02080.0289-0.03620.0340.0471-0.21270.00050.35170.0010.02240.4847-0.05560.2475-4.2045-13.9949-39.3775
31.441-0.3224-1.6451.88551.39265.59090.0075-0.29030.01550.1620.11930.13630.0896-0.3307-0.12110.3812-0.0304-0.06211.1486-0.01060.4178-1.2821-17.45031.8354
48.6225-1.28-3.48381.6358-0.31366.5781-0.2924-0.4328-0.28520.5865-0.2638-0.24670.28260.27130.56670.51710.0187-0.11210.9639-0.06580.44098.1521-15.9804-0.2069
52.3539-1.0458-1.35072.11110.48464.8988-0.3274-0.43140.24690.41230.1307-0.12480.0759-0.21010.20640.42090.0224-0.09481.0532-0.07690.4754-2.041-15.7061.1698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 858 through 1023 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1024 through 1342 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 52 )
4X-RAY DIFFRACTION4chain 'B' and (resid 53 through 76 )
5X-RAY DIFFRACTION5chain 'B' and (resid 77 through 120 )

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