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- PDB-6kuw: Crystal structure of human alpha2C adrenergic G protein-coupled r... -

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Basic information

Entry
Database: PDB / ID: 6kuw
TitleCrystal structure of human alpha2C adrenergic G protein-coupled receptor.
ComponentsAlpha-2C adrenergic receptor
KeywordsSIGNALING PROTEIN / Alpha2c adrenergic receptor / antagonist / GPCR
Function / homology
Function and homology information


alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / receptor transactivation / epinephrine binding / negative regulation of norepinephrine secretion / alpha-2A adrenergic receptor binding / negative regulation of epinephrine secretion / regulation of smooth muscle contraction / Surfactant metabolism / Adrenoceptors ...alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / receptor transactivation / epinephrine binding / negative regulation of norepinephrine secretion / alpha-2A adrenergic receptor binding / negative regulation of epinephrine secretion / regulation of smooth muscle contraction / Surfactant metabolism / Adrenoceptors / adrenergic receptor signaling pathway / regulation of vasoconstriction / negative regulation of insulin secretion / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of neuron differentiation / activation of protein kinase B activity / guanyl-nucleotide exchange factor activity / platelet activation / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / cell-cell signaling / G alpha (i) signalling events / positive regulation of MAPK cascade / endosome / protein heterodimerization activity / G protein-coupled receptor signaling pathway / protein homodimerization activity / plasma membrane / cytoplasm
Similarity search - Function
Alpha 2C adrenoceptor / Glycosyl transferases group 1 / Adrenoceptor family / 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)
Similarity search - Domain/homology
CHOLESTEROL / Chem-E33 / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Alpha-2C adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, X.Y. / Wu, L.J. / Wu, D. / Zhong, G.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31771130 China
CitationJournal: To Be Published
Title: Crystal structure of human alpha2C adrenergic G protein-coupled receptor.
Authors: Chen, X.Y. / Wu, D. / Wu, L.J. / Han, G.W. / Guo, Y. / Zhong, G.S.
History
DepositionSep 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-2C adrenergic receptor
B: Alpha-2C adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,58015
Polymers111,0172
Non-polymers4,56313
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-13 kcal/mol
Surface area44610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.480, 78.740, 190.450
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 , 1 types, 2 molecules AB

#1: Protein Alpha-2C adrenergic receptor


Mass: 55508.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P18825*PLUS

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Non-polymers , 5 types, 15 molecules

#2: Chemical ChemComp-E33 / (8~{a}~{R},12~{a}~{S},13~{a}~{R})-12-ethylsulfonyl-3-methoxy-5,6,8,8~{a},9,10,11,12~{a},13,13~{a}-decahydroisoquinolino[2,1-g][1,6]naphthyridine


Mass: 364.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28N2O3S
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#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 ligand of interestY
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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: sodium phosphate monobasic (0.1M), Hepes pH6.5-6.9 (0.1M), PEG400 24-35%

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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: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 26778 / % possible obs: 94.4 % / Redundancy: 3.74 % / Biso Wilson estimate: 79.97 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.127 / Net I/σ(I): 8.15
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.23 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1692 / CC1/2: 0.604 / % possible all: 82.1
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4s0v

4s0v


Resolution: 2.8→47.04 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.389
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1302 4.86 %RANDOM
Rwork0.213 ---
obs0.216 26777 94.4 %-
Displacement parametersBiso mean: 65 Å2
Baniso -1Baniso -2Baniso -3
1--6.353 Å20 Å20 Å2
2--2.8413 Å20 Å2
3---3.5116 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.8→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7370 0 243 2 7615
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097819HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0910596HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2669SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1275HARMONIC5
X-RAY DIFFRACTIONt_it7819HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion20.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion999SEMIHARMONIC5
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_contact9309SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.91 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3088 137 5.23 %
Rwork0.2242 2483 -
all0.2285 2620 -
obs--83.15 %
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)
10.79130.23850.72991.61430.61633.711-0.0429-0.0058-0.0128-0.0950.00440.0260.0654-0.21930.0385-0.0142-0.0397-0.002-0.1668-0.0017-0.2213-33.664-14.845342.5422
23.10140.0118-0.83674.75561.4489.7294-0.22450.4141-0.3984-0.5396-0.1411-0.5338-0.0761-0.08570.36560.3163-0.14230.16-0.257-0.043-0.4493-22.5118-26.5342-4.8486
31.5677-0.1863-0.47761.53240.44483.5257-0.11670.13690.174-0.27130.2219-0.2212-0.610.817-0.1051-0.1098-0.18020.0533-0.0674-0.0344-0.2769-7.92624.546543.2563
45.2038-1.4977-1.21955.5791.1897.7060.1983-0.18340.1528-0.3868-0.4140.0932-1.0885-0.62970.21580.27340.26570.0628-0.09290.0026-0.4832-16.711512.3845-6.7691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|41 - 454 }
2X-RAY DIFFRACTION2{ A|1001 - 1196 }
3X-RAY DIFFRACTION3{ B|41 - 453 }
4X-RAY DIFFRACTION4{ B|1001 - 1196 }

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