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- PDB-5zty: Crystal structure of human G protein coupled receptor -

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Basic information

Entry
Database: PDB / ID: 5zty
TitleCrystal structure of human G protein coupled receptor
ComponentsG protein coupled receptor,T4 lysozyme,G protein coupled receptor
KeywordsMEMBRANE PROTEIN / GPCR / cell signaling / ligand design
Function / homology
Function and homology information


cannabinoid receptor activity / negative regulation of mast cell activation / negative regulation of synaptic transmission, GABAergic / negative regulation of action potential / Class A/1 (Rhodopsin-like receptors) / regulation of metabolic process / leukocyte chemotaxis / extrinsic component of cytoplasmic side of plasma membrane / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / viral release from host cell by cytolysis ...cannabinoid receptor activity / negative regulation of mast cell activation / negative regulation of synaptic transmission, GABAergic / negative regulation of action potential / Class A/1 (Rhodopsin-like receptors) / regulation of metabolic process / leukocyte chemotaxis / extrinsic component of cytoplasmic side of plasma membrane / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / viral release from host cell by cytolysis / response to amphetamine / peptidoglycan catabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (i) signalling events / perikaryon / host cell cytoplasm / response to lipopolysaccharide / defense response to bacterium / inflammatory response / immune response / dendrite / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Cannabinoid receptor type 2 / Cannabinoid receptor 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. ...Cannabinoid receptor type 2 / Cannabinoid receptor 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. / 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
Similarity search - Domain/homology
Chem-9JU / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Endolysin / Cannabinoid receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, X.T. / Hua, T. / Wu, L.J. / Liu, Z.J.
CitationJournal: Cell / Year: 2019
Title: Crystal Structure of the Human Cannabinoid Receptor CB2
Authors: Li, X. / Hua, T. / Vemuri, K. / Ho, J.H. / Wu, Y. / Wu, L. / Popov, P. / Benchama, O. / Zvonok, N. / Locke, K. / Qu, L. / Han, G.W. / Iyer, M.R. / Cinar, R. / Coffey, N.J. / Wang, J. / Wu, M. ...Authors: Li, X. / Hua, T. / Vemuri, K. / Ho, J.H. / Wu, Y. / Wu, L. / Popov, P. / Benchama, O. / Zvonok, N. / Locke, K. / Qu, L. / Han, G.W. / Iyer, M.R. / Cinar, R. / Coffey, N.J. / Wang, J. / Wu, M. / Katritch, V. / Zhao, S. / Kunos, G. / Bohn, L.M. / Makriyannis, A. / Stevens, R.C. / Liu, Z.J.
History
DepositionMay 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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 6, 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: G protein coupled receptor,T4 lysozyme,G protein coupled receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,33316
Polymers56,1961
Non-polymers3,13715
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-41 kcal/mol
Surface area24490 Å2
Unit cell
Length a, b, c (Å)34.295, 106.240, 183.403
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein G protein coupled receptor,T4 lysozyme,G protein coupled receptor / Lysis protein / Lysozyme


Mass: 56195.910 Da / Num. of mol.: 1
Fragment: UNP residues 21-222,UNP residues 1-161,UNP residues 235-352
Mutation: G78L, T127A, T153l,C1053T, C1096A,R242E, G304E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34972, UniProt: D9IEF7, lysozyme

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Non-polymers , 8 types, 64 molecules

#2: Chemical ChemComp-9JU / N-(adamantan-1-yl)-1-(5-hydroxypentyl)-4-methyl-5-phenyl-1H-pyrazole-3-carboxamide


Mass: 421.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H35N3O2
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 63.03 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.2
Details: 100mM sodium cacodylate trihydrate pH 6.2, 40% PEG400, 400mM lithium sulfate monohydrate
PH range: 6.0-6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.96 Å / Num. obs: 17142 / % possible obs: 96.93 % / Redundancy: 7.8 % / Biso Wilson estimate: 76.06 Å2 / CC1/2: 0.99 / Net I/σ(I): 14.7
Reflection shellResolution: 2.8→2.9 Å / Num. unique all: 11117 / Num. unique obs: 1576 / CC1/2: 0.87 / % possible all: 92.81

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RH1

2rh1


Resolution: 2.8→29.91 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.029 / SU Rfree Blow DPI: 0.365 / SU Rfree Cruickshank DPI: 0.365
RfactorNum. reflection% reflectionSelection details
Rfree0.275 856 5.08 %RANDOM
Rwork0.224 ---
obs0.226 16854 97.1 %-
Displacement parametersBiso max: 236.41 Å2 / Biso mean: 95.84 Å2 / Biso min: 31.49 Å2
Baniso -1Baniso -2Baniso -3
1-18.7312 Å20 Å20 Å2
2---24.3229 Å20 Å2
3---5.5918 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 2.8→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 169 49 3726
Biso mean--115.25 61.01 -
Num. residues----449
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1310SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes594HARMONIC5
X-RAY DIFFRACTIONt_it3770HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion477SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3956SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3770HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5102HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.14
X-RAY DIFFRACTIONt_other_torsion18.79
LS refinement shellResolution: 2.8→2.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3287 151 5.21 %
Rwork0.2708 2746 -
all0.274 2897 -
obs--94.89 %
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)
11.83080.0885-0.31381.1756-0.87166.4443-0.05570.1859-0.0045-0.0466-0.0557-0.0593-0.38490.12570.1114-0.3225-0.00260.04450.53740.0747-0.437410.7085-1.5521-43.4207
22.0909-0.1078-0.18730.58730.7321.94730.0128-0.2290.5013-0.04820.06170.0175-0.43420.0764-0.0746-0.281-0.02760.03320.3826-0.0125-0.39867.716-18.2516.797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|19 - A|319 }A19 - 319
2X-RAY DIFFRACTION2{ A|1001 - A|1060 }A1001 - 1060

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