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- PDB-4zjc: Structures of the human OX1 orexin receptor bound to selective an... -

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Basic information

Entry
Database: PDB / ID: 4zjc
TitleStructures of the human OX1 orexin receptor bound to selective and dual antagonists
Componentshuman OX1R fusion protein to P.abysii glycogen synthase
KeywordsSIGNALING PROTEIN / Orexin / suvorexant / SB-674042 / MEMBRANE PROTEIN-Transferase complex
Function / homology
Function and homology information


orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / glycogen (starch) synthase activity / feeding behavior / glycogen biosynthetic process / peptide hormone binding / neuropeptide signaling pathway / cellular response to hormone stimulus / regulation of cytosolic calcium ion concentration / G protein-coupled receptor activity ...orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / glycogen (starch) synthase activity / feeding behavior / glycogen biosynthetic process / peptide hormone binding / neuropeptide signaling pathway / cellular response to hormone stimulus / regulation of cytosolic calcium ion concentration / G protein-coupled receptor activity / peptide binding / G alpha (q) signalling events / chemical synaptic transmission / positive regulation of ERK1 and ERK2 cascade / synapse / plasma membrane / cytosol
Similarity search - Function
Orexin/Hypocretin receptor type 1 / Orexin receptor family / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Orexin/Hypocretin receptor type 1 / Orexin receptor family / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / 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
Chem-4OT / OLEIC ACID / Orexin/Hypocretin receptor type 1 / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.832 Å
AuthorsYin, J. / Brautigam, C.A. / Shao, Z. / Clark, L. / Harrell, C.M. / Gotter, A.L. / Coleman, P.J. / Renger, J.J. / Rosenbaum, D.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure and ligand-binding mechanism of the human OX1 and OX2 orexin receptors.
Authors: Yin, J. / Babaoglu, K. / Brautigam, C.A. / Clark, L. / Shao, Z. / Scheuermann, T.H. / Harrell, C.M. / Gotter, A.L. / Roecker, A.J. / Winrow, C.J. / Renger, J.J. / Coleman, P.J. / Rosenbaum, D.M.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: human OX1R fusion protein to P.abysii glycogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6984
Polymers62,6851
Non-polymers1,0133
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.431, 66.466, 182.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein human OX1R fusion protein to P.abysii glycogen synthase


Mass: 62685.031 Da / Num. of mol.: 1
Fragment: UNP O43613 residues 1-245,UNP Q9V2J8 residues 218-413,UNP O43613 residues 288-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Gene: HCRTR1, PAB2292, PYRAB00770 / Plasmid: pFastbac1 / Strain: GE5 / Orsay / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43613, UniProt: Q9V2J8
#2: Chemical ChemComp-4OT / [5-(2-fluorophenyl)-2-methyl-1,3-thiazol-4-yl]{(2S)-2-[(5-phenyl-1,3,4-oxadiazol-2-yl)methyl]pyrrolidin-1-yl}methanone


Mass: 448.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21FN4O2S
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2

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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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6
Details: 100 mM Sodium Citrate pH 5.6, 32% PEG 400, 200 mM Potossium

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→44.83 Å / Num. obs: 18893 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S0V,2BFW

4s0v

2bfw


Resolution: 2.832→44.825 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2618 806 5.32 %
Rwork0.2163 --
obs0.2187 15148 79.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.832→44.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4027 0 49 0 4076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034175
X-RAY DIFFRACTIONf_angle_d0.6675646
X-RAY DIFFRACTIONf_dihedral_angle_d10.2721533
X-RAY DIFFRACTIONf_chiral_restr0.023628
X-RAY DIFFRACTIONf_plane_restr0.003728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8318-3.00920.3173590.2802970X-RAY DIFFRACTION33
3.0092-3.24150.33321160.27341678X-RAY DIFFRACTION58
3.2415-3.56750.29191390.25242545X-RAY DIFFRACTION85
3.5675-4.08350.2611470.21182971X-RAY DIFFRACTION99
4.0835-5.14360.25771690.19543035X-RAY DIFFRACTION100
5.1436-44.8310.22221760.20113143X-RAY DIFFRACTION99
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)
14.66971.47370.74936.64991.30145.21980.2743-0.50540.48050.4251-0.09990.5732-0.5386-0.1531-0.02370.52330.0003-0.01170.1799-0.15860.3324-1.71070.9939-81.9567
25.64482.346-4.21849.676-5.95425.1806-0.98682.0812-1.088-0.3523-0.18431.0081.2426-0.86750.961.0905-0.53150.48771.2716-0.51341.375613.0244.0551-63.2366
31.1318-0.7378-0.08352.3931.41450.9706-0.1042-0.2473-0.07930.5540.1883-0.22850.52520.2159-0.55920.53460.0954-0.04340.1968-0.20470.1915.4425-5.1903-41.048
41.7616-0.1541-0.91541.83412.61125.0495-0.0582-0.2547-0.11780.3153-0.0868-0.12990.6893-0.16650.07870.60410.13230.02150.1025-0.21980.0667-2.3953-6.177-42.9393
50.6343-0.637-0.39690.91290.14851.2710.0359-0.0366-0.0165-0.0006-0.00580.1230.2466-0.3980.0810.4704-0.07820.15930.3443-0.18610.0101-13.23761.522-36.4786
68.7003-3.9462-1.6655.86172.44639.12680.5965-0.1099-0.96871.1806-0.41382.0820.6205-0.2841-0.23991.3329-0.39260.11030.93-0.05950.9535-16.8312-5.1696-23.8155
72.05070.35360.07081.54420.1320.0118-0.07540.2233-0.14090.1013-0.52310.39170.1762-0.22560.34410.3863-0.01860.01780.3996-0.16780.1391-15.968-5.7878-49.5083
80.0683-0.2426-0.59251.82951.92675.0761-0.2798-0.1092-0.0361-0.2609-0.46330.8665-0.992-1.67650.4660.68250.1876-0.09760.8899-0.33760.3397-12.555-3.6645-70.6387
92.04450.92160.27771.834-0.8750.74350.26420.41770.6484-0.4281-0.76370.2583-0.7558-0.66060.00590.5630.2939-0.08370.5113-0.1640.2991-16.68947.8157-49.9662
107.04896.84936.04237.18846.16735.3427-0.4185-0.39510.6388-0.2601-0.4060.7764-0.5775-0.44610.53290.41570.10980.0580.31550.03910.1603-10.77717.3282-27.1128
118.5351-5.27145.90418.3383-4.66664.2880.2184-0.2949-0.6759-0.14750.29740.91191.0457-0.5722-0.52690.3040.0083-0.04110.33540.04240.22616.208917.957-4.7774
124.60991.12751.5862.6652-2.07033.0799-0.2017-1.07270.49490.81650.06480.0835-0.5520.00590.19770.3927-0.0032-0.10.6148-0.07010.1211.594125.440613.667
132.5217-0.3841-1.08182.77451.46963.134-0.0294-0.43620.77230.1573-0.02890.2476-1.1927-0.18960.04580.68970.0375-0.03990.4163-0.31550.3849-10.80936.40846.5879
146.1638-1.1084-0.86774.4054-0.82821.72660.0808-0.33850.6143-0.0905-0.0035-0.3617-0.8180.19490.0060.3785-0.0138-0.02320.1941-0.1090.1411-1.25828.16010.9776
158.8533-0.4346-0.72682.3487-0.42168.79940.18170.2933-0.2074-0.0712-0.10830.34540.2502-0.6133-0.09750.29350.0468-0.01790.1695-0.02290.051-11.039720.0151-3.1824
160.8730.1543-0.51862.05560.18932.83910.0398-0.7265-0.19350.4704-0.12180.1970.4391-0.40490.09250.52590.04370.0690.52630.05130.0445-10.01516.17725.9122
171.50640.1396-0.58422.19810.40872.4129-0.1341-0.05840.0053-0.4159-0.22390.1454-0.3815-0.24990.1030.66380.1121-0.07020.3151-0.09140.0343-5.302310.3311-38.4863
186.54241.2255-1.0740.2288-0.20180.17570.13322.6165-0.3383-2.0359-0.0062-0.5256-0.48420.0681-0.31971.95370.17620.32510.8857-0.09480.6909-3.015310.3613-66.3142
192.4772-0.36371.33284.0069-0.39456.10040.1437-0.12480.08690.0211-0.0111-0.19340.4908-0.0103-0.17250.2950.05880.030.2873-0.1270.16212.61093.3989-40.6496
206.01961.9612-2.25387.8731-5.83414.43920.3671-1.06040.8442-0.1388-0.377-0.08181.13361.98220.14391.15820.2181-0.25310.7028-0.21880.51769.8992-4.4996-26.139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 26:40 )A26 - 40
2X-RAY DIFFRACTION2( CHAIN A AND RESID 41:47 )A41 - 47
3X-RAY DIFFRACTION3( CHAIN A AND RESID 48:72 )A48 - 72
4X-RAY DIFFRACTION4( CHAIN A AND RESID 73:116 )A73 - 116
5X-RAY DIFFRACTION5( CHAIN A AND RESID 117:154 )A117 - 154
6X-RAY DIFFRACTION6( CHAIN A AND RESID 155:162 )A155 - 162
7X-RAY DIFFRACTION7( CHAIN A AND RESID 163:187 )A163 - 187
8X-RAY DIFFRACTION8( CHAIN A AND RESID 188:211 )A188 - 211
9X-RAY DIFFRACTION9( CHAIN A AND RESID 212:228 )A212 - 228
10X-RAY DIFFRACTION10( CHAIN A AND RESID 229:245 )A229 - 245
11X-RAY DIFFRACTION11( CHAIN A AND RESID 246:246 ) or ( CHAIN A AND RESID 1001:1011 )A246
12X-RAY DIFFRACTION12( CHAIN A AND RESID 1012:1036 )A1012 - 1036
13X-RAY DIFFRACTION13( CHAIN A AND RESID 1037:1096 )A1037 - 1096
14X-RAY DIFFRACTION14( CHAIN A AND RESID 1097:1121 )A1097 - 1121
15X-RAY DIFFRACTION15( CHAIN A AND RESID 1122:1162 )A1122 - 1162
16X-RAY DIFFRACTION16( CHAIN A AND RESID 1163:1196 )A1163 - 1196
17X-RAY DIFFRACTION17( CHAIN A AND RESID 288:324 )A288 - 324
18X-RAY DIFFRACTION18( CHAIN A AND RESID 325:339 )A325 - 339
19X-RAY DIFFRACTION19( CHAIN A AND RESID 340:365 )A340 - 365
20X-RAY DIFFRACTION20( CHAIN A AND RESID 366:373 )A366 - 373

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