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- PDB-4ldl: Structure of beta2 adrenoceptor bound to hydroxybenzylisoproteren... -

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Basic information

Entry
Database: PDB / ID: 4ldl
TitleStructure of beta2 adrenoceptor bound to hydroxybenzylisoproterenol 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 / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / norepinephrine binding / positive regulation of autophagosome maturation / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity ...beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / norepinephrine binding / positive regulation of autophagosome maturation / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / response to psychosocial stress / endosome to lysosome transport / adrenergic receptor signaling pathway / diet induced thermogenesis / positive regulation of protein kinase A signaling / neuronal dense core vesicle / adenylate cyclase binding / smooth muscle contraction / bone resorption / 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 / response to cold / peptidoglycan catabolic process / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / positive regulation of protein serine/threonine kinase activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / lysozyme activity / positive regulation of cold-induced thermogenesis / Clathrin-mediated endocytosis / amyloid-beta binding / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / lysosome / early endosome / receptor complex / cell surface receptor signaling pathway / 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 / 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 / Phage lysozyme / Lysozyme domain superfamily / 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-XQC / 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: 3.1 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)67,0615
Polymers66,4202
Non-polymers6413
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-19 kcal/mol
Surface area28200 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 / 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 / Plasmid: pVl1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / 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, 5 molecules

#3: Chemical ChemComp-XQC / 4-[(1R)-1-hydroxy-2-{[1-(4-hydroxyphenyl)-2-methylpropan-2-yl]amino}ethyl]benzene-1,2-diol


Mass: 317.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23NO4
#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.: 2 / 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: 9

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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: 3.1→33.3 Å / Num. obs: 18053 / % possible obs: 94.5 % / Observed criterion σ(F): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 6.2
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1789 / % possible all: 95.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1243)refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LDE

4lde


Resolution: 3.1→33.265 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 876 5.1 %Same as 4LDE
Rwork0.229 ---
obs0.2303 18053 90.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→33.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 39 2 4514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034622
X-RAY DIFFRACTIONf_angle_d0.596274
X-RAY DIFFRACTIONf_dihedral_angle_d9.2811604
X-RAY DIFFRACTIONf_chiral_restr0.042722
X-RAY DIFFRACTIONf_plane_restr0.002781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.19120.39141280.36322379X-RAY DIFFRACTION86
3.1912-3.29410.33191220.34512361X-RAY DIFFRACTION84
3.2941-3.41170.37891310.31922515X-RAY DIFFRACTION91
3.4117-3.54820.29631390.29252572X-RAY DIFFRACTION91
3.5482-3.70950.29961350.25812583X-RAY DIFFRACTION94
3.7095-3.90480.25391270.23862557X-RAY DIFFRACTION91
3.9048-4.1490.2411470.21392587X-RAY DIFFRACTION92
4.149-4.46860.18461360.1832533X-RAY DIFFRACTION93
4.4686-4.9170.25831430.18432551X-RAY DIFFRACTION92
4.917-5.62560.23841340.19892488X-RAY DIFFRACTION90
5.6256-7.07640.22991350.23172529X-RAY DIFFRACTION90
7.0764-33.26650.21161430.18272496X-RAY DIFFRACTION91
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)
15.07745.40550.64786.92431.65482.5219-0.02930.2568-0.2740.21550.1828-0.22790.08580.1006-0.23490.47330.0483-0.02360.3899-0.00850.5518-16.0277-29.5091-77.6583
22.14470.1270.86741.2527-1.00265.23290.0288-0.27860.12740.152-0.0910.0126-0.25910.11870.05530.47040.02890.02850.4905-0.07440.3481-3.4208-10.994-40.5645
35.1644-0.1757-0.64874.0982-0.68430.7526-0.1014-0.5535-0.2791-0.0702-0.2211-0.72850.058-0.48340.32580.5409-0.0037-0.02330.9991-0.2430.57490.0598-25.3169-35.7801
47.7266-4.5322-5.12725.0315-1.39312.0013-0.72071.15421.0556-0.85060.3387-0.34310.40190.560.38121.053-0.0893-0.25861.6877-0.05230.93541.3955-24.7169-60.271
53.7363-1.0201-3.40533.5731.02328.4024-0.20310.1277-0.15750.4691-0.46270.35250.6228-1.86240.64850.5458-0.19920.00070.8207-0.1170.4203-12.2479-17.1836-33.7019
61.8306-0.6207-1.32452.86392.84468.00490.0730.1073-0.05470.12430.0709-0.05360.04740.1429-0.07450.4557-0.0805-0.04431.03240.02790.4648-1.1181-17.45811.839
74.79210.3587-0.43680.86590.14215.0293-0.05690.5008-0.34820.0752-0.0677-0.01140.32630.62210.0520.8515-0.0929-0.13671.2072-0.18360.54068.2045-16.1964-0.1657
83.8177-2.0715-2.02143.21790.81872.792-0.2609-0.5220.09390.55460.27090.02190.076-1.07330.08040.59090.0682-0.02751.1065-0.02650.5391-1.8949-15.69561.158
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 1231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1263 through 1298 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1299 through 1304 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1305 through 1342 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 76 )
8X-RAY DIFFRACTION8chain 'B' and (resid 77 through 120 )

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