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- PDB-5d5a: In meso in situ serial X-ray crystallography structure of the Bet... -

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Basic information

Entry
Database: PDB / ID: 5d5a
TitleIn meso in situ serial X-ray crystallography structure of the Beta2-adrenergic receptor at 100 K
ComponentsBeta-2 adrenergic receptor,Endolysin,Beta-2 adrenergic receptor
KeywordsMembrane Protein/Hydrolase / MEMBRANE PROTEIN / HYDROLASE / Membrane Protein-Hydrolase complex
Function / homology
Function and homology information


positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / AMPA selective glutamate receptor signaling pathway / norepinephrine binding / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction ...positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / AMPA selective glutamate receptor signaling pathway / norepinephrine binding / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of multicellular organism growth / adrenergic receptor signaling pathway / response to psychosocial stress / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / bone resorption / positive regulation of bone mineralization / potassium channel regulator activity / brown fat cell differentiation / intercellular bridge / viral release from host cell by cytolysis / 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 / amyloid-beta binding / positive regulation of cold-induced thermogenesis / microtubule cytoskeleton / G alpha (s) signalling events / transcription by RNA polymerase II / host cell cytoplasm / early endosome / lysosome / receptor complex / cell surface receptor signaling pathway / positive regulation of MAPK cascade / endosome / endosome membrane / Ub-specific processing proteases / ciliary basal body / defense response to bacterium / cilium / 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 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. ...Beta 2 adrenoceptor / Adrenoceptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / 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)
Similarity search - Domain/homology
beta-maltose / ACETAMIDE / 1,4-BUTANEDIOL / Chem-CAU / CHOLESTEROL / PALMITIC ACID / Endolysin / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4826 Å
AuthorsHuang, C.-Y. / Olieric, V. / Warshamanage, R. / Liu, X. / Kobilka, B. / Kay Diederichs, K. / Wang, M. / Caffrey, M.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.
Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, M.
History
DepositionAug 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-2 adrenergic receptor,Endolysin,Beta-2 adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,02117
Polymers56,6011
Non-polymers3,41916
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-75 kcal/mol
Surface area22580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.000, 170.000, 40.500
Angle α, β, γ (deg.)90.00, 106.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1308-

HOH

21A-1327-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 56601.438 Da / Num. of mol.: 1
Mutation: N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A,N187E, C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ADRB2, ADRB2R, B2AR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: P00720, lysozyme
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 8 types, 68 molecules

#3: Chemical ChemComp-CAU / (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol / (S)-Carazolol


Mass: 298.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O2
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#8: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30-35 %(v/v) PEG 400, 0.1-0.2 M Na2SO4, 0.1 M bis-tris propane pH 6.5-7.0 and 5-7 %(v/v) 1,4-butanediol
PH range: pH 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0322 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0322 Å / Relative weight: 1
ReflectionResolution: 2.4826→50 Å / Num. obs: 23086 / % possible obs: 95.1 % / Redundancy: 5.7 % / Net I/σ(I): 7.27
Reflection shellResolution: 2.4826→2.57 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.11 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rh1

2rh1


Resolution: 2.4826→43.96 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2623 1155 5 %
Rwork0.2116 --
obs0.2142 23086 94.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4826→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 210 53 3809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063842
X-RAY DIFFRACTIONf_angle_d1.4875219
X-RAY DIFFRACTIONf_dihedral_angle_d17.8641376
X-RAY DIFFRACTIONf_chiral_restr0.031596
X-RAY DIFFRACTIONf_plane_restr0.019614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4826-2.59560.3521330.32842466X-RAY DIFFRACTION85
2.5956-2.73250.35261400.29832757X-RAY DIFFRACTION95
2.7325-2.90360.3181440.2622817X-RAY DIFFRACTION96
2.9036-3.12780.27881490.24952760X-RAY DIFFRACTION95
3.1278-3.44240.27971410.22882752X-RAY DIFFRACTION95
3.4424-3.94020.26171470.20072810X-RAY DIFFRACTION97
3.9402-4.96320.22591480.18872802X-RAY DIFFRACTION96
4.9632-43.9670.24291530.17872767X-RAY DIFFRACTION95

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