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- PDB-4s0v: Crystal structure of the human OX2 orexin receptor bound to the i... -

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Basic information

Entry
Database: PDB / ID: 4s0v
TitleCrystal structure of the human OX2 orexin receptor bound to the insomnia drug Suvorexant
ComponentsHuman Orexin receptor type 2 fusion protein to P. abysii Glycogen Synthase
KeywordsSIGNALING PROTEIN / G protein-coupled receptor / orexin neurotransmitters / orexin receptor / Orexin-A / Orexin-B / Suvorexant / N-linked glycosylation
Function / homology
Function and homology information


regulation of circadian sleep/wake cycle, wakefulness / circadian sleep/wake cycle process / orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / neuropeptide receptor activity / locomotion / feeding behavior / peptide hormone binding / neuropeptide signaling pathway ...regulation of circadian sleep/wake cycle, wakefulness / circadian sleep/wake cycle process / orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / neuropeptide receptor activity / locomotion / feeding behavior / peptide hormone binding / neuropeptide signaling pathway / regulation of cytosolic calcium ion concentration / cellular response to hormone stimulus / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / G alpha (q) signalling events / synapse / nucleoplasm / plasma membrane
Similarity search - Function
Orexin receptor 2 / Orexin receptor type 2 / 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. ...Orexin receptor 2 / Orexin receptor type 2 / 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 receptor type 2 / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYin, J. / Kolb, P. / Mobarec, J.C. / Rosenbaum, D.M.
CitationJournal: Nature / Year: 2015
Title: Crystal structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant.
Authors: Yin, J. / Mobarec, J.C. / Kolb, P. / Rosenbaum, D.M.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionJan 14, 2015ID: 4RNB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 20, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human Orexin receptor type 2 fusion protein to P. abysii Glycogen Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8233
Polymers64,0901
Non-polymers7332
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.358, 75.819, 96.335
Angle α, β, γ (deg.)90.00, 111.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Human Orexin receptor type 2 fusion protein to P. abysii Glycogen Synthase / Ox-2-R / Ox2-R / Ox2R / Hypocretin receptor type 2 / Glycogen synthase


Mass: 64089.777 Da / Num. of mol.: 1
Fragment: UNP O43614 residues 3-254, 294-388, and UNP Q9V2J8 residues 218-413
Source method: isolated from a genetically manipulated source
Details: MOLECULE IS AN ENGINEERED FUSION PROTEIN IN WHICH THE 196-AMINO-ACID CATALYTIC DOMAIN OF PYROCOCCUS ABYSII GLYCOGEN SYNTHASE REPLACES 39 RESIDUES AT THE INTRAC ELLULAR LOOP 3 (ICL3) OF THE ...Details: MOLECULE IS AN ENGINEERED FUSION PROTEIN IN WHICH THE 196-AMINO-ACID CATALYTIC DOMAIN OF PYROCOCCUS ABYSII GLYCOGEN SYNTHASE REPLACES 39 RESIDUES AT THE INTRAC ELLULAR LOOP 3 (ICL3) OF THE HUMAN OX2 OREXIN RECEPTOR
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi GE5 (archaea)
Gene: HCRTR2, PAB2292, PYRAB00770 / Plasmid: pFastbac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43614, 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.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 52

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.9
Details: 31% PEG 400, 0.1 M sodium citrate, 0.2 M sodium formate, 3%(w/v) hexanediol, pH 5.9, Lipidic Cubic Phase (LCP), temperature 293K

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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: Jul 24, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 22305 / Num. obs: 22305 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.54 Å / % possible all: 99

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1839)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4DKL and 2BFW

4dkl

2bfw


Resolution: 2.5→43.717 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 955 5.09 %RANDOM
Rwork0.1972 ---
obs0.1972 18772 84.19 %-
all-19767 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→43.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 40 28 3878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043939
X-RAY DIFFRACTIONf_angle_d0.7455331
X-RAY DIFFRACTIONf_dihedral_angle_d12.361437
X-RAY DIFFRACTIONf_chiral_restr0.025611
X-RAY DIFFRACTIONf_plane_restr0.003648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61990.2862400.2457994X-RAY DIFFRACTION32
2.6199-2.7840.29191120.23291928X-RAY DIFFRACTION65
2.784-2.99890.26911460.23112758X-RAY DIFFRACTION92
2.9989-3.30060.28411560.22023003X-RAY DIFFRACTION100
3.3006-3.77790.24371710.19533029X-RAY DIFFRACTION100
3.7779-4.75890.2291680.17113018X-RAY DIFFRACTION100
4.7589-43.7170.21021620.18953087X-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)
11.5733-1.34062.40121.5019-1.86654.06850.0033-0.29990.40440.1249-0.0290.32290.06570.87610.0510.7827-0.0884-0.08490.7261-0.15240.622254.143326.520761.3854
20.71130.05960.05732.39591.43194.5987-0.17480.13350.36-0.1194-0.29770.4591-0.26420.0790.09510.23950.0094-0.04080.17390.03550.261542.911418.346437.8261
30.5902-0.7036-0.9381.0389-0.89214.14220.0527-0.12990.0552-0.0086-0.090.1935-0.2621-0.04330.02660.1485-0.00870.01350.2252-0.02790.260844.838210.981746.5369
42.05260.3682-1.90581.41770.21644.50320.157-0.0876-0.0872-0.0870.0211-0.1786-0.07560.3297-0.11020.12930.0323-0.00860.1977-0.01080.243650.69972.311639.8424
54.49881.6653-0.75240.6239-0.34770.5012-0.6997-0.8659-0.9418-0.84990.5674-0.05020.27770.67080.05320.55490.0837-0.0520.6739-0.03190.6351.1587-3.73321.8609
61.1427-0.4149-0.25182.23630.85663.7473-0.095-0.1175-0.09820.2434-0.19620.42360.43540.10660.19560.1625-0.03210.03750.22750.0130.30246.62930.309852.9248
78.5317-5.5758-2.83126.16110.85512.12990.0116-0.85540.21320.36430.4551-0.84220.01130.20120.03820.39280.0444-0.08970.48230.05390.33454.88820.803564.3297
80.39710.30010.38542.3335-0.44646.01420.0260.1252-0.1344-0.26540.025-0.18050.29780.4550.03650.27360.09620.03350.3630.02470.282963.18722.489436.7223
92.4840.25280.08145.6862-2.873.74630.0015-0.65360.30410.59020.26861.07320.0472-0.5921-0.07610.55090.05310.08120.4787-0.07770.312465.448915.10242.948
105.6591-2.0191-1.89664.0350.98854.0781-0.22620.55370.3664-0.4563-0.02090.0465-0.01070.12540.20460.3063-0.0670.01050.2569-0.00320.231768.50311.4582-17.7986
113.0099-1.1395-0.33943.0154-1.95941.7347-0.5026-0.6766-0.20290.3263-0.0923-0.61940.48440.4420.41570.59930.089-0.01110.33130.07250.298672.9179-4.811-4.38
122.76840.1383-0.49526.2111-0.51931.1261-0.49340.8921-0.322-0.6056-0.19960.34261.22920.04550.09720.708-0.03280.15390.0902-0.09750.378968.2344-7.9264-18.43
131.3292-1.62630.7882.8743-2.08882.353-0.5179-0.325-0.55030.4228-0.3974-0.93020.74181.2697-0.56810.3520.31170.12490.53080.14420.605981.0025-5.0721-7.6087
142.1047-0.2233-0.15275.15343.15573.83270.0171-0.27480.0713-0.77390.2874-0.7054-0.40810.91690.00940.2512-0.02380.02320.38690.05120.353877.15565.667-9.3649
151.68440.5376-0.07262.0340.83780.3814-0.1927-0.32720.33340.0190.01210.22840.83890.51110.07660.36260.03940.01530.29570.00740.138166.81640.9472-4.3766
162.5842-0.31150.88481.92082.08246.90090.5588-0.588-0.16720.9042-0.41470.11230.1911-0.76020.27830.6726-0.0482-0.04510.40770.01550.623766.38981.49477.1544
172.2123-1.05060.59942.72871.69613.2468-0.0401-0.3816-0.26590.3202-0.27450.56880.6299-0.48470.2450.3308-0.0460.07480.28550.01940.35959.3061-2.0919-5.3341
180.59910.37480.88390.77041.75783.4917-0.27730.12310.1139-0.0193-0.1442-0.029-0.4923-0.21710.23660.34350.00540.04140.39940.01590.251255.713710.25826.9053
190.80950.2174-0.76822.6163-0.69131.3894-0.1134-0.27310.09030.3497-0.2711-0.3922-0.35380.64390.36970.19-0.0389-0.01730.36730.00360.308361.997510.786249.4395
200.5420.0760.18321.5576-0.31293.21890.1773-0.15390.1453-0.0755-0.14640.0835-0.4567-0.1967-0.11690.2847-0.0040.00180.2269-0.0210.271850.461519.172738.4349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 50:54)
2X-RAY DIFFRACTION2(chain A and resid 55:85)
3X-RAY DIFFRACTION3(chain A and resid 86:124)
4X-RAY DIFFRACTION4(chain A and resid 125:156)
5X-RAY DIFFRACTION5(chain A and resid 157:168)
6X-RAY DIFFRACTION6(chain A and resid 169:206)
7X-RAY DIFFRACTION7(chain A and resid 207:220)
8X-RAY DIFFRACTION8(chain A and resid 221:252)
9X-RAY DIFFRACTION9(chain A and (resid 253:254) or (resid 1001: 1012))
10X-RAY DIFFRACTION10(chain A and resid 1013:1031)
11X-RAY DIFFRACTION11(chain A and resid 1032:1053)
12X-RAY DIFFRACTION12(chain A and resid 1054:1069)
13X-RAY DIFFRACTION13(chain A and resid 1070:1087)
14X-RAY DIFFRACTION14(chain A and resid 1088:1107)
15X-RAY DIFFRACTION15(chain A and resid 1108:1121)
16X-RAY DIFFRACTION16(chain A and resid 1122:1127)
17X-RAY DIFFRACTION17(chain A and resid 1128:1182)
18X-RAY DIFFRACTION18(chain A and (resid 1183:1196) or (resid 294:304))
19X-RAY DIFFRACTION19(chain A and resid 305:340)
20X-RAY DIFFRACTION20(chain A and resid 341:381)

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