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- PDB-5ws3: Crystal structures of human orexin 2 receptor bound to the select... -

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Basic information

Entry
Database: PDB / ID: 5ws3
TitleCrystal structures of human orexin 2 receptor bound to the selective antagonist EMPA determined by serial femtosecond crystallography at SACLA
ComponentsOrexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2
KeywordsSIGNALING PROTEIN / receptor
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 / G alpha (q) signalling events / chemical synaptic transmission / 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
Chem-7MA / OLEIC ACID / Orexin receptor type 2 / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSuno, R. / Kimura, K. / Nakane, T. / Yamashita, K. / Wang, J. / Fujiwara, T. / Yamanaka, Y. / Im, D. / Tsujimoto, H. / Sasanuma, M. ...Suno, R. / Kimura, K. / Nakane, T. / Yamashita, K. / Wang, J. / Fujiwara, T. / Yamanaka, Y. / Im, D. / Tsujimoto, H. / Sasanuma, M. / Horita, 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.
Funding support Japan, 4items
OrganizationGrant numberCountry
JST Japan
MEXT Japan
JSPS26102725 Japan
JSPS15H04338 Japan
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
DepositionDec 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jun 20, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 23, 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: Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2668
Polymers64,2051
Non-polymers2,0617
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint0 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.510, 75.980, 96.100
Angle α, β, γ (deg.)90.00, 112.30, 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


Mass: 64204.871 Da / Num. of mol.: 1
Fragment: UNP residues 3-254,UNP residues 218-413,UNP residues 294-388
Source method: isolated from a genetically manipulated source
Details: Chimera protein of UNP residues 3-254 from Orexin receptor type 2 (O43614), UNP residues 218-413 from GlgA glycogen synthase (Q9V2J8), UNP residues 294-388 from Orexin receptor type 2 (O43614)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Gene: HCRTR2, PAB2292 / Strain: GE5 / Orsay / 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


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


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


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 0.1M MES, 0.1M sodium malonate, 27-30% PEG 300, pH 6.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å
DetectorType: MPCCD / Detector: CCD / Date: Apr 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 28958 / % possible obs: 100 % / Redundancy: 77.6 % / CC1/2: 0.98 / Net I/σ(I): 5.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.2 % / CC1/2: 0.58 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
Cheetah3.22data extraction
CrystFELdata processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4s0v

4s0v


Resolution: 2.3→45.109 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 1440 4.97 %
Rwork0.1988 --
obs0.1999 28958 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→45.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 121 12 4196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054310
X-RAY DIFFRACTIONf_angle_d0.7145814
X-RAY DIFFRACTIONf_dihedral_angle_d11.8642586
X-RAY DIFFRACTIONf_chiral_restr0.047651
X-RAY DIFFRACTIONf_plane_restr0.004708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.43611340.39742742X-RAY DIFFRACTION100
2.3822-2.47760.36791300.32022740X-RAY DIFFRACTION100
2.4776-2.59030.31221450.26462719X-RAY DIFFRACTION100
2.5903-2.72690.2971440.2382748X-RAY DIFFRACTION100
2.7269-2.89770.22641390.20022734X-RAY DIFFRACTION100
2.8977-3.12140.23231510.19782748X-RAY DIFFRACTION100
3.1214-3.43540.23861590.19392763X-RAY DIFFRACTION100
3.4354-3.93220.1931310.17982752X-RAY DIFFRACTION100
3.9322-4.95320.1931450.17482768X-RAY DIFFRACTION100
4.9532-45.11730.20281620.19712804X-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)
11.15860.0548-0.05662.4917-0.12643.025-0.08790.1059-0.0111-0.0685-0.0104-0.0417-0.0711-0.06620.08880.55610.00670.09710.46140.00120.570146.276940.0896-46.8419
20.32970.1314-1.08120.0966-0.54773.69960.01150.0157-0.028-0.0572-0.0494-0.0457-0.0962-0.09890.04820.76320.00680.06610.5345-0.01330.580339.647.049-39.435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 251 )
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 383 )

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