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- PDB-5wqc: Crystal structure of human orexin 2 receptor bound to the selecti... -

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Basic information

Entry
Database: PDB / ID: 5wqc
TitleCrystal structure of human orexin 2 receptor bound to the selective antagonist EMPA determined by the synchrotron light source at SPring-8.
ComponentsOrexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2
KeywordsSIGNALING PROTEIN / G PROTEIN-COUPLED RECEPTOR / OREXIN NEUROTRANSMITTERS / OREXIN 2 RECEPTOR / OREXIN-A / OREXIN-B / EMPA / 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 / neuropeptide receptor activity / glycogen (starch) synthase activity / feeding behavior / locomotion / 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 / neuropeptide receptor activity / glycogen (starch) synthase activity / feeding behavior / locomotion / peptide hormone binding / neuropeptide signaling pathway / cellular response to hormone stimulus / regulation of cytosolic calcium ion concentration / peptide binding / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / chemical synaptic transmission / nucleotide binding / synapse / 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 / Glycogen Phosphorylase B; / Serpentine type 7TM GPCR chemoreceptor Srsx ...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 / Glycogen Phosphorylase B; / 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) / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7MA / OLEIC ACID / Orexin receptor type 2 / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSuno, R. / Hirata, K. / Yamashita, K. / Tsujimoto, H. / Sasanuma, M. / Horita, S. / Yamamoto, M. / Rosenbaum, D.M. / Iwata, S. / Shimamura, T. / Kobayashi, T.
Funding support Japan, United States, 12items
OrganizationGrant numberCountry
Japan Science and Technology Agency (JST)target-driven R&D (A-STEP) Japan
Japan Science and Technology Agency (JST)the Research Acceleration Program Japan
Toray Science Foundation Japan
Takeda Science Foundation Japan
the Naito Foundation Japan
Ministry of Education, Culture, Sports, Science and Technology (MEXT)the Platform for Drug Discovery, Informatics, and Structural Life Science (PDIS) Japan
the Ministry of Education, Culture, Sports, Science and Technology (MEXT)the X-ray Free-Electron Laser Priority Strategy Program Japan
JSPS26102725 Japan
JSPS15H04338 Japan
JSPS15K08268 Japan
JSPS15H06862 Japan
the Welch FoundationI-1770 United States
CitationJournal: Structure / Year: 2018
Title: Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA
Authors: Suno, R. / Kimura, K.T. / Nakane, T. / Yamashita, K. / Wang, J. / Fujiwara, T. / Yamanaka, Y. / Im, D. / Horita, S. / Tsujimoto, H. / Tawaramoto, M.S. / Hirokawa, T. / Nango, E. / Tono, K. / ...Authors: Suno, R. / Kimura, K.T. / Nakane, T. / Yamashita, K. / Wang, J. / Fujiwara, T. / Yamanaka, Y. / Im, D. / Horita, S. / Tsujimoto, H. / Tawaramoto, M.S. / Hirokawa, T. / Nango, E. / Tono, K. / Kameshima, T. / Hatsui, T. / Joti, Y. / Yabashi, M. / Shimamoto, K. / Yamamoto, M. / Rosenbaum, D.M. / Iwata, S. / Shimamura, T. / Kobayashi, T.
History
DepositionNov 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3108
Polymers64,2051
Non-polymers2,1057
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-1 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.130, 75.520, 95.930
Angle α, β, γ (deg.)90.00, 111.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2 / Ox2R / Hypocretin receptor type 2 / Glycogen synthase / Ox2R / Hypocretin receptor type 2


Mass: 64204.871 Da / Num. of mol.: 1
Fragment: UNP residues 3-254,UNP residues 218-413,UNP residues 294-386
Source method: isolated from a genetically manipulated source
Details: chimera of human orexin receptor type 2 and Pyrococcus abyssi GE5 GlgA glycogen synthase
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi GE5 (archaea)
Gene: HCRTR2, PAB2292 / Strain: GE5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43614, UniProt: Q9V2J8
#2: Chemical ChemComp-7MA / N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide / EMPA (drug)


Mass: 454.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N4O4S / Comment: antagonist*YM
#3: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 50 mM MES-NaOH (pH 5.8-6.2), 26-29% PEG300, 100 mM sodium malonate, 0.5 mM EMPA, 5% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Apr 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→46.65 Å / Num. obs: 45007 / % possible obs: 99.99 % / Redundancy: 47.8 % / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→46.641 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 2272 5.05 %
Rwork0.181 --
obs0.1827 45004 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→46.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 133 126 4271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154275
X-RAY DIFFRACTIONf_angle_d1.2285763
X-RAY DIFFRACTIONf_dihedral_angle_d14.922580
X-RAY DIFFRACTIONf_chiral_restr0.08646
X-RAY DIFFRACTIONf_plane_restr0.008696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.00260.37281410.32362660X-RAY DIFFRACTION100
2.0026-2.04920.33051400.27152648X-RAY DIFFRACTION100
2.0492-2.10040.29451510.23822646X-RAY DIFFRACTION100
2.1004-2.15720.23311390.21092677X-RAY DIFFRACTION100
2.1572-2.22070.23491450.19242649X-RAY DIFFRACTION100
2.2207-2.29230.23111290.18032643X-RAY DIFFRACTION100
2.2923-2.37430.22261470.17212667X-RAY DIFFRACTION100
2.3743-2.46930.22111460.1612637X-RAY DIFFRACTION100
2.4693-2.58170.20981450.16222676X-RAY DIFFRACTION100
2.5817-2.71780.20851500.15412668X-RAY DIFFRACTION100
2.7178-2.88810.21311480.16142659X-RAY DIFFRACTION100
2.8881-3.1110.20981470.16522664X-RAY DIFFRACTION100
3.111-3.4240.19041310.17072696X-RAY DIFFRACTION100
3.424-3.91920.20281250.16922693X-RAY DIFFRACTION100
3.9192-4.93690.20261380.17162706X-RAY DIFFRACTION100
4.9369-46.6540.19221500.19112743X-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)
11.57060.0714-0.21622.32370.28681.59150.0020.1185-0.026-0.1321-0.0354-0.035-0.1153-0.0940.03570.28660.01510.03210.1138-0.00590.23744.17839.416-46.1238
22.69960.3895-0.25983.9801-0.55763.0133-0.07280.112-0.1589-0.0515-0.0263-0.01180.1511-0.01750.07930.30480.00120.03850.1332-0.01270.216526.168832.43727.0706
30.32670.01740.26260.1098-0.84542.1648-0.0757-0.0931-0.01290.0864-0.0751-0.0012-0.36610.1660.12430.34580.02110.05830.22770.00810.259336.471942.1453-23.7082
42.84530.82761.54724.66591.76825.626-0.08930.14530.1632-0.0506-0.04230.0574-0.46980.03030.18260.30730.03720.08990.09310.01070.237340.652149.863-43.9708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 251 )
2X-RAY DIFFRACTION2chain 'A' and (RESID 252:254 OR RESID 1001:1181 )
3X-RAY DIFFRACTION3chain 'A' and (RESID 1182:1196 OR RESID 294:328 )
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 383 )

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