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- PDB-3pbl: Structure of the human dopamine D3 receptor in complex with eticl... -

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Basic information

Entry
Database: PDB / ID: 3pbl
TitleStructure of the human dopamine D3 receptor in complex with eticlopride
ComponentsD(3) dopamine receptor, Lysozyme chimera
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Structural Genomics / PSI-2 / PSI-Biology / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / 7TM / G protein-coupled receptor / GPCR / GPCR Network / Signal transduction / Hydrolase / eticlopride / dopamine / neurotransmitter / chimera / T4L fusion / Membrane protein / transmembrane / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


musculoskeletal movement, spinal reflex action / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / response to histamine / regulation of potassium ion transport / Dopamine receptors / adenylate cyclase-inhibiting dopamine receptor signaling pathway / regulation of dopamine uptake involved in synaptic transmission / positive regulation of dopamine receptor signaling pathway / phospholipase C-activating dopamine receptor signaling pathway ...musculoskeletal movement, spinal reflex action / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / response to histamine / regulation of potassium ion transport / Dopamine receptors / adenylate cyclase-inhibiting dopamine receptor signaling pathway / regulation of dopamine uptake involved in synaptic transmission / positive regulation of dopamine receptor signaling pathway / phospholipase C-activating dopamine receptor signaling pathway / negative regulation of oligodendrocyte differentiation / negative regulation of synaptic transmission, glutamatergic / G protein-coupled receptor internalization / response to morphine / arachidonic acid secretion / dopamine metabolic process / regulation of dopamine secretion / negative regulation of cytosolic calcium ion concentration / positive regulation of cytokinesis / behavioral response to cocaine / social behavior / negative regulation of protein secretion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / prepulse inhibition / adenylate cyclase-activating adrenergic receptor signaling pathway / viral release from host cell by cytolysis / negative regulation of blood pressure / positive regulation of mitotic nuclear division / peptidoglycan catabolic process / locomotory behavior / response to cocaine / learning / G protein-coupled receptor activity / circadian regulation of gene expression / visual learning / intracellular calcium ion homeostasis / adenylate cyclase-activating dopamine receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (i) signalling events / host cell cytoplasm / learning or memory / defense response to bacterium / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / synapse / plasma membrane
Similarity search - Function
Dopamine D3 receptor / Dopamine receptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme ...Dopamine D3 receptor / Dopamine receptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / Chem-ETQ / Endolysin / D(3) dopamine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsChien, E.Y.T. / Liu, W. / Han, G.W. / Katritch, V. / Zhao, Q. / Cherezov, V. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR)
CitationJournal: Science / Year: 2010
Title: Structure of the human dopamine d3 receptor in complex with a d2/d3 selective antagonist.
Authors: Chien, E.Y. / Liu, W. / Zhao, Q. / Katritch, V. / Han, G.W. / Hanson, M.A. / Shi, L. / Newman, A.H. / Javitch, J.A. / Cherezov, V. / Stevens, R.C.
History
DepositionOct 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 9, 2012Group: Structure summary
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.label_entity_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.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D(3) dopamine receptor, Lysozyme chimera
B: D(3) dopamine receptor, Lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6726
Polymers107,3062
Non-polymers1,3664
Water0
1
A: D(3) dopamine receptor, Lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3363
Polymers53,6531
Non-polymers6832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D(3) dopamine receptor, Lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3363
Polymers53,6531
Non-polymers6832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.828, 92.492, 176.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein D(3) dopamine receptor, Lysozyme chimera / Dopamine D3 receptor / Endolysin / Lysis protein / Muramidase


Mass: 53653.047 Da / Num. of mol.: 2 / Mutation: L119W, C1054T, C1097A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: DRD3, E / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P35462, UniProt: P00720, lysozyme
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ETQ / 3-chloro-5-ethyl-N-{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxy-2-methoxybenzamide


Mass: 340.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25ClN2O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 45

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: Lipidic cubic phase made of monoolein and 10% cholesterol, 30% PEG400, 300mM Ammonium acetate, 2% glucose, 100mM bis tris propane pH 7.5, 1mM eticlopride, LIPIDIC CUBIC PHASE, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2010 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 26229 / % possible obs: 78.5 % / Redundancy: 7.7 % / Biso Wilson estimate: 48.31 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 0.8 / Rsym value: 0.99 / % possible all: 32.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RH1

2rh1


Resolution: 2.89→36.45 Å / Cor.coef. Fo:Fc: 0.8883 / Cor.coef. Fo:Fc free: 0.8548 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 1318 5.1 %RANDOM
Rwork0.2432 ---
obs0.2447 25845 --
Displacement parametersBiso mean: 76.45 Å2
Baniso -1Baniso -2Baniso -3
1--3.4913 Å20 Å20 Å2
2--0.7412 Å20 Å2
3---2.7501 Å2
Refine analyzeLuzzati coordinate error obs: 0.586 Å
Refinement stepCycle: LAST / Resolution: 2.89→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6695 0 92 0 6787
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00969412
X-RAY DIFFRACTIONt_angle_deg1.0894622
X-RAY DIFFRACTIONt_dihedral_angle_d22952
X-RAY DIFFRACTIONt_trig_c_planes1192
X-RAY DIFFRACTIONt_gen_planes10115
X-RAY DIFFRACTIONt_it684520
X-RAY DIFFRACTIONt_nbd05
X-RAY DIFFRACTIONt_omega_torsion4.97
X-RAY DIFFRACTIONt_other_torsion16.55
X-RAY DIFFRACTIONt_chiral_improper_torsion9275
X-RAY DIFFRACTIONt_ideal_dist_contact83304
LS refinement shellResolution: 2.89→3.01 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2864 48 4.23 %
Rwork0.2678 1088 -
all0.2685 1136 -
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)
12.09410.46071.68582.724-0.06967.39320.0612-0.0288-0.09250.0731-0.0412-0.17580.54420.0957-0.02-0.09930.0363-0.056-0.03530.0918-0.20784.7976-14.0348-1.9304
22.08892.7453-0.56268.31542.41526.4425-0.18290.1327-0.1822-0.24880.2827-0.1628-0.0561-0.326-0.0998-0.13370.0088-0.0413-0.2610.0498-0.29385.50734.2583-43.7494
31.7410.58412.52636.4693-0.45863.4020.0521-0.2087-0.2072-0.0863-0.03910.1340.1772-0.0594-0.01290.2148-0.152-0.1520.11780.1243-0.1288-3.4354-20.3907-4.2989
42.6235-1.1982-1.67673.60531.49726.7173-0.0085-0.09290.31280.01840.0959-0.241-0.46410.1454-0.0874-0.2539-0.0591-0.0035-0.00160.0093-0.19276.332412.51492.5559
58.3154-0.69741.42485.89790.56416.8090.0102-0.3413-0.45340.13620.0312-0.04260.54420.2359-0.04130.04890.1063-0.0897-0.0127-0.1274-0.0989-13.662819.801148.5178
64.0113-0.0541-2.91046.84930.27891.78390.0376-0.13480.3897-0.0097-0.0395-0.1295-0.19380.09340.00190.26350.03930.0641-0.02720.0032-0.12114.491622.90233.4233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|32 - A|221 }A32 - 221
2X-RAY DIFFRACTION2{ A|1002 - A|1161 }A1002 - 1161
3X-RAY DIFFRACTION3{ A|319 - A|400 }A319 - 400
4X-RAY DIFFRACTION4{ B|32 - B|221 }B32 - 221
5X-RAY DIFFRACTION5{ B|1002 - B|1161 }B1002 - 1161
6X-RAY DIFFRACTION6{ B|319 - B|400 }B319 - 400

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