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- PDB-4ldo: Structure of beta2 adrenoceptor bound to adrenaline and an engine... -

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Basic information

Entry
Database: PDB / ID: 4ldo
TitleStructure of beta2 adrenoceptor bound to adrenaline 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


positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / AMPA selective glutamate receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / norepinephrine binding / Adrenoceptors / positive regulation of lipophagy ...positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / AMPA selective glutamate receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / norepinephrine binding / Adrenoceptors / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / endosome to lysosome transport / response to psychosocial stress / adrenergic receptor signaling pathway / diet induced thermogenesis / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / bone resorption / positive regulation of bone mineralization / potassium channel regulator activity / neuronal dense core vesicle / brown fat cell differentiation / viral release from host cell by cytolysis / intercellular bridge / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / peptidoglycan catabolic process / receptor-mediated endocytosis / response to cold / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / cell wall macromolecule catabolic process / mitotic spindle / lysozyme / lysozyme activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / microtubule cytoskeleton / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / early endosome / cell surface receptor signaling pathway / lysosome / receptor complex / positive regulation of MAPK cascade / endosome / endosome membrane / Ub-specific processing proteases / defense response to bacterium / cilium / ciliary basal body / apical plasma membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / membrane / 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. / Lysozyme-like domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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 / 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: 3.2 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_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_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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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)66,9506
Polymers66,4202
Non-polymers5304
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-18 kcal/mol
Surface area27860 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, 6 molecules

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


Mass: 183.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 41

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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-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2013
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: 3.2→33.3 Å / Num. obs: 16359 / % possible obs: 92.7 % / Observed criterion σ(F): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 6
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1411 / % possible all: 78.8

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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: 3.2→33.265 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 758 5.05 %Same as 4LDE
Rwork0.2224 ---
obs0.2241 16359 86.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→33.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4433 0 30 2 4465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034571
X-RAY DIFFRACTIONf_angle_d0.5956212
X-RAY DIFFRACTIONf_dihedral_angle_d9.9051566
X-RAY DIFFRACTIONf_chiral_restr0.043720
X-RAY DIFFRACTIONf_plane_restr0.002777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-3.31450.32441100.29552249X-RAY DIFFRACTION72
3.3145-3.4470.31131250.29292506X-RAY DIFFRACTION84
3.447-3.60370.34841420.28362654X-RAY DIFFRACTION87
3.6037-3.79350.32311420.25652672X-RAY DIFFRACTION88
3.7935-4.03080.2681410.22332664X-RAY DIFFRACTION88
4.0308-4.34140.23441450.20152696X-RAY DIFFRACTION89
4.3414-4.77710.23131520.18572690X-RAY DIFFRACTION88
4.7771-5.46580.25481450.19862694X-RAY DIFFRACTION89
5.4658-6.87630.24281350.25412690X-RAY DIFFRACTION89
6.8763-33.26640.21531560.19612658X-RAY DIFFRACTION88
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)
18.59215.10631.27344.817-0.19913.90.09030.34210.20610.02370.3177-0.021-0.05950.6345-0.33990.61520.00910.04990.4804-0.00810.62-10.6885-21.0561-76.4016
28.58545.1156-0.24019.4579-2.54846.2880.01110.3364-0.39860.50740.29560.13610.4169-0.1975-0.23660.6833-0.070.02350.3641-0.09820.6264-21.9904-38.2967-78.7018
31.58840.20540.01571.08720.06975.33280.0404-0.31410.01410.0322-0.0731-0.0334-0.27640.14970.08010.58810.00470.02290.55510.00320.4357-3.4649-10.7268-40.519
43.4054-1.74041.57435.51712.58763.1404-0.23850.1755-0.3117-0.0211-0.30650.26560.331-0.49610.70240.6268-0.159-0.0570.7519-0.03420.6162-9.4226-17.8757-38.6352
52.94880.2493-0.14761.50661.80037.1940.1255-0.12150.0784-0.1190.1655-0.0127-0.06470.473-0.25450.73110.0314-0.05581.04160.0940.54090.874-16.43051.325
63.96543.4148-0.265.6681-5.09738.7198-0.42190.7492-2.3604-1.00250.0935-0.68151.93540.25640.19821.13430.0133-0.06291.0164-0.28240.99197.5875-23.21350.3895
77.95511.95825.07026.35194.41824.9406-0.19580.03260.23271.12210.3986-0.25590.42750.2709-0.16740.79240.24070.01191.0371-0.07590.59230.731-14.49055.222
83.2852-3.94932.3935.5353-5.40739.83240.5954-0.3662-0.70210.88020.1102-0.2527-0.77350.007-0.5880.57420.0112-0.08140.78-0.02380.657-3.1113-19.7768-18.322
98.29990.32641.90275.74054.36267.6978-0.0423-0.38890.17440.1042-0.31450.5271-0.3788-1.58290.69690.62420.07660.06650.967-0.02850.8071-6.4466-16.28293.7923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 858 through 945 )
2X-RAY DIFFRACTION2chain 'A' and (resid 946 through 1023 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1024 through 1295 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1296 through 1342 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 66 )
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 76 )
7X-RAY DIFFRACTION7chain 'B' and (resid 77 through 99 )
8X-RAY DIFFRACTION8chain 'B' and (resid 100 through 106 )
9X-RAY DIFFRACTION9chain 'B' and (resid 107 through 120 )

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