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- PDB-4zj8: Structures of the human OX1 orexin receptor bound to selective an... -

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Basic information

Entry
Database: PDB / ID: 4zj8
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 / SB674042
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
OLEIC ACID / Chem-SUV / Orexin/Hypocretin receptor type 1 / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.751 Å
AuthorsYin, J. / Brautigam, C.A. / Shao, Z. / Clark, L. / Harrell, C.M. / Gotter, A.L. / Coleman, P. / 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)64,8318
Polymers62,6851
Non-polymers2,1467
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.242, 64.992, 181.478
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
Details (production host): Molecule is an engineered fusion protein in which the 196-amino-acid catalytic domain of Pyroccus abysii glycogen synthase replace 31 residues at the intracellular loop 3 ...Details (production host): Molecule is an engineered fusion protein in which the 196-amino-acid catalytic domain of Pyroccus abysii glycogen synthase replace 31 residues at the intracellular loop 3 (ICL3) of the human OX1 orexin receptor
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43613, UniProt: Q9V2J8
#2: Chemical ChemComp-SUV / [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone / suvorexant


Mass: 450.921 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23ClN6O2 / Comment: medication, antagonist*YM
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.4
Details: 100mM Sodium Citrate pH 5.4, 31% PEG 400, 200 mM Sodium Formate

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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: 2.75→43.75 Å / Num. obs: 20480 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.2
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.19 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedev_1951data collection
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S0V,2BFW

4s0v

2bfw


Resolution: 2.751→43.714 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 828 5.31 %Random selection
Rwork0.2227 ---
obs0.2254 15601 77.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.751→43.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4027 0 90 18 4135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034212
X-RAY DIFFRACTIONf_angle_d0.7325684
X-RAY DIFFRACTIONf_dihedral_angle_d10.8331557
X-RAY DIFFRACTIONf_chiral_restr0.024628
X-RAY DIFFRACTIONf_plane_restr0.003731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7506-2.92290.3273330.2665832X-RAY DIFFRACTION26
2.9229-3.14850.3463870.27781521X-RAY DIFFRACTION48
3.1485-3.46520.32711570.26272741X-RAY DIFFRACTION88
3.4652-3.96630.26891750.22293158X-RAY DIFFRACTION100
3.9663-4.9960.24711820.19773189X-RAY DIFFRACTION100
4.996-43.71990.25441940.2113332X-RAY DIFFRACTION100
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)
16.15570.952.48197.364-2.07817.43780.2609-0.61631.05370.5571-0.07350.3984-0.8118-0.5519-0.18530.59320.157-0.01820.3637-0.14580.4368-2.38051.218-82.1274
28.59130.02385.40522.90072.26725.96960.57690.57850.495-0.91020.3292-0.1351.2651-0.7885-0.94651.4435-0.51460.25741.3972-0.17590.754312.55853.5801-63.3248
30.4298-0.3043-0.23330.81260.59730.52270.0346-0.1393-0.15690.25620.0613-0.12650.47610.04910.12570.53150.0550.01090.4097-0.3103-0.0069-4.5206-3.2858-40.1631
48.4744-1.9704-1.50412.5677-3.31756.6408-0.5526-1.0383-0.8951.38430.09880.78551.8147-1.28280.43521.1057-0.2840.24790.79-0.07880.5207-16.3476-5.1431-27.8882
51.80480.89473.60633.79820.71287.76730.02850.3846-0.1783-0.64150.12670.08710.16080.3858-0.14610.384-0.05710.00680.7022-0.4030.5438-18.3198-4.7293-47.9562
60.1830.35550.03410.78910.49265.7294-0.0652-0.00550.1077-0.1834-0.15780.3178-0.2092-0.9630.15350.58390.0039-0.07140.7111-0.21110.2026-9.375-6.4859-70.9978
73.7874-0.43971.86881.6074-1.88122.7016-0.5433-0.62370.8258-1.3276-0.23621.2522-1.9698-1.53460.81791.09490.4309-0.42641.2968-0.52780.8996-19.1145-0.21-63.8641
81.87980.8588-0.48322.144-1.48182.7762-0.01520.404-0.1141-0.6564-0.07410.4921-0.0217-0.65280.13790.69830.4234-0.24160.7354-0.25280.3598-17.74517.3312-51.7952
96.92764.14154.67848.10965.18137.1434-0.32840.11970.3336-0.3393-0.3310.4904-0.4787-0.24550.52150.26790.11960.05260.22370.06030.118-10.083617.082-26.3932
101.20710.19330.95871.43130.97595.1788-0.0979-0.44070.24520.1942-0.09450.0823-0.1154-0.16170.1330.2262-0.021-0.09160.6165-0.06190.12345.236921.77116.8028
111.81320.3444-1.31241.33380.55514.15280.0311-0.53590.80130.03790.00260.2374-1.3996-0.3375-0.01330.58670.119-0.05770.5735-0.21810.267-7.58932.65145.3165
126.5651-0.1532-0.72253.94840.04984.2509-0.1901-0.1184-0.1645-0.11030.10970.54120.1276-0.63220.0480.19110.048-0.02720.34440.00070.0782-10.951919.3836-3.025
133.703-2.6382-1.72725.2947-0.91095.8635-0.19390.104-0.23730.64260.07370.4416-0.0185-0.10120.16060.37550.01110.13390.8607-0.15770.2917-15.662420.872811.1461
140.9094-0.15460.12930.8153-0.11461.3733-0.0227-0.1566-0.10680.1551-0.0378-0.01460.14250.02420.00110.4294-0.0061-0.06160.38610.14170.0696-4.133810.8185-0.1207
153.96430.2927-0.71622.66251.32815.3121-0.0956-0.2630.09580.162-0.08540.0405-0.19230.0634-0.01430.43020.0055-0.05720.3118-0.10160.0693-2.562810.897-22.3788
160.4224-0.06-0.07771.17630.4710.99050.0640.22990.0127-0.7134-0.2650.3245-0.3904-0.36110.18430.85390.1182-0.00440.2692-0.10790.1556-7.289210.0798-49.786
172.959-1.1959-3.12533.9682.33353.62990.16522.2759-0.6953-1.224-0.0633-0.3632-0.5238-0.316-0.11461.98830.13950.03291.0823-0.06721.0425-4.659611.2277-68.4733
189.0537-3.7932-6.07241.75763.12866.10130.09361.1393-0.4249-0.4378-0.15430.1287-0.3502-0.25150.04161.4032-0.0777-0.00710.5313-0.10820.37960.33937.8087-60.7562
190.6609-0.322-0.61310.18920.04972.59080.0426-0.14620.0890.00530.0616-0.13450.00830.2612-0.01220.34170.02910.04320.3338-0.19610.1562.91823.6207-40.4858
209.7389-0.52391.39430.9304-2.78538.33850.5301-1.1424-0.05930.69380.186-0.70390.38041.7891-0.69191.01340.115-0.31430.8905-0.24980.53168.3982-3.5306-25.6051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 26:39)
2X-RAY DIFFRACTION2(chain A and resid 40:48)
3X-RAY DIFFRACTION3(chain A and resid 49:153)
4X-RAY DIFFRACTION4(chain A and resid 154:169)
5X-RAY DIFFRACTION5(chain A and resid 170:179)
6X-RAY DIFFRACTION6(chain A and resid 180:203)
7X-RAY DIFFRACTION7(chain A and resid 204:208)
8X-RAY DIFFRACTION8(chain A and resid 209:228)
9X-RAY DIFFRACTION9(chain A and resid 229:246)
10X-RAY DIFFRACTION10(chain A and resid 1001:1029)
11X-RAY DIFFRACTION11(chain A and resid 1030:1122)
12X-RAY DIFFRACTION12(chain A and resid 1123:1162)
13X-RAY DIFFRACTION13(chain A and resid 1163:1180)
14X-RAY DIFFRACTION14(chain A and (resid 1181:1196) or (resid 288:288))
15X-RAY DIFFRACTION15(chain A and resid 289:301)
16X-RAY DIFFRACTION16(chain A and resid 302:325)
17X-RAY DIFFRACTION17(chain A and resid 326:334)
18X-RAY DIFFRACTION18(chain A and resid 335:341)
19X-RAY DIFFRACTION19(chain A and resid 342:363)
20X-RAY DIFFRACTION20(chain A and resid 364:373)

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