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- PDB-6kpc: Crystal structure of an agonist bound GPCR -

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Basic information

Entry
Database: PDB / ID: 6kpc
TitleCrystal structure of an agonist bound GPCR
ComponentsCannabinoid receptor 2,Endolysin,Cannabinoid receptor 2
KeywordsMEMBRANE PROTEIN / GPCR / LCP / agonist
Function / homology
Function and homology information


cannabinoid signaling pathway / cannabinoid receptor activity / negative regulation of mast cell activation / regulation of metabolic process / negative regulation of nitric-oxide synthase activity / negative regulation of synaptic transmission, GABAergic / negative regulation of action potential / leukocyte chemotaxis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled receptor activity ...cannabinoid signaling pathway / cannabinoid receptor activity / negative regulation of mast cell activation / regulation of metabolic process / negative regulation of nitric-oxide synthase activity / negative regulation of synaptic transmission, GABAergic / negative regulation of action potential / leukocyte chemotaxis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled receptor activity / response to amphetamine / adenylate cyclase-activating G protein-coupled receptor signaling pathway / sensory perception of pain / viral release from host cell by cytolysis / peptidoglycan catabolic process / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of inflammatory response / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / cytolysis / perikaryon / response to lipopolysaccharide / host cell cytoplasm / immune response / inflammatory response / G protein-coupled receptor signaling pathway / defense response to bacterium / dendrite / endoplasmic reticulum / integral component of plasma membrane / plasma membrane / cytoplasm
7 transmembrane receptor (rhodopsin family) / Cannabinoid receptor type 2 / Phage lysozyme / G protein-coupled receptor, rhodopsin-like / T4-type lysozyme / Endolysin T4 type / Lysozyme-like domain superfamily / GPCR, rhodopsin-like, 7TM / Cannabinoid receptor family / Glycoside hydrolase, family 24
Endolysin / Cannabinoid receptor 2
Biological speciesHomo sapiens (human)
Enterobacteria phage RB59 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLi, X.T. / Hua, T. / Wu, L.J. / Makriyannis, A. / Wu, M. / Liu, Z.J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cannabinoid receptor 2,Endolysin,Cannabinoid receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6562
Polymers56,2101
Non-polymers4461
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)33.960, 140.220, 156.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cannabinoid receptor 2,Endolysin,Cannabinoid receptor 2 / hCB2 / CX5 / Lysis protein / Lysozyme / Muramidase / hCB2 / CX5


Mass: 56209.934 Da / Num. of mol.: 1
Mutation: G78L, T127A, T153L, G210A, C54T, C97A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, C54T, C97A, R242E, G304E,G78L, ...Mutation: G78L, T127A, T153L, G210A, C54T, C97A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, C54T, C97A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, C54T, C97A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E,G78L, T127A, T153L, G210A, R242E, G304E
Source method: isolated from a genetically manipulated source
Details: CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 ...Details: CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion,CB2, T4 lysozyme, CB2 fusion
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB59 (bacteriophage)
Gene: CNR2, CB2A, CB2B, e, RB59_126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34972, UniProt: A0A097J809, lysozyme
#2: Chemical ChemComp-8D0 / (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol


Mass: 445.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H39NO3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.31 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM HEPES sodium pH 7.0, 25% PEG 400, 220 mM Sodium sulfate decahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→44.78 Å / Num. obs: 11476 / % possible obs: 87.6 % / Redundancy: 2.847 % / Biso Wilson estimate: 96.93 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.171 / Rrim(I) all: 0.2 / Χ2: 0.994 / Net I/σ(I): 4.26 / Num. measured all: 32673 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.2-3.282.7960.6731.2223859448530.6270.78990.4
3.28-3.373.0650.5991.5325999388480.6390.69790.4
3.37-3.472.70.5561.5820258857500.7350.66484.7
3.47-3.582.7780.4212.0420758457470.8990.49588.4
3.58-3.73.1320.4192.7324658737870.8480.48290.1
3.7-3.822.8670.313.2321198297390.8870.36589.1
3.82-3.972.7220.323.3318627686840.9030.3889.1
3.97-4.132.8750.2584.1920217807030.940.390.1
4.13-4.312.9110.2514.6919277386620.9410.29389.7
4.31-4.532.5230.2084.9115396906100.9370.24988.4
4.53-4.772.8440.1945.8916986935970.9470.22786.1
4.77-5.062.8510.1995.7915856305560.9640.23188.3
5.06-5.412.8760.1955.9914816095150.950.22784.6
5.41-5.842.920.1855.8814605735000.9750.21787.3
5.84-6.42.9690.1626.2913515194550.9580.18887.7
6.4-7.162.810.1546.9111694904160.9560.18384.9
7.16-8.262.8270.1458.6810464333700.9330.16985.5
8.26-10.122.6030.1228.817943683050.9570.14682.9
10.12-14.312.7470.0899.476733062450.9880.10380.1
14.31-44.782.9780.0749.883991881340.9950.08671.3
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zty
Resolution: 3.2→44.78 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.48
RfactorNum. reflection% reflectionSelection details
Rfree0.262 531 4.63 %RANDOM
Rwork0.23 ---
Obs0.231 11475 87.7 %-
Displacement parametersBiso max: 262.08 Å2 / Biso mean: 118.21 Å2 / Biso min: 11.04 Å2
Baniso -1Baniso -2Baniso -3
1-20.7169 Å20 Å20 Å2
2---22.8308 Å20 Å2
3---2.1138 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: final / Resolution: 3.2→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 29 0 3500
Biso mean--114.15 --
Num. residues----445
Refine LS restraints
Refinement-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1211SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes578HARMONIC5
X-RAY DIFFRACTIONt_it3581HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion473SEMIHARMONIC5
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_contact4227SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3581HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4871HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion1.95
X-RAY DIFFRACTIONt_other_torsion19.89
LS refinement shellResolution: 3.2→3.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2744 130 4.83 %
Rwork0.2316 2560 -
All0.2337 2690 -
Obs--88.31 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.1904-1.0658-0.37887.0911-5.820810.97730.18120.01180.15150.1045-0.5129-0.2743-0.63840.84620.3318-0.4219-0.05990.0676-0.11010.304-0.313310.6139-2.8231-32.6508
24.27570.0526-1.6961.13690.59831.75620.1452-0.54180.37250.18310.07990.1184-0.15730.0554-0.225-0.1209-0.05780.04580.0746-0.1068-0.2662-5.1493-22.92519.9196
Refinement TLS group
IDRefinement-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|19 - 315 }A19 - 315
2X-RAY DIFFRACTION2{ A|1001 - 1160 }A1001 - 1160

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