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- PDB-7lig: The structure of the insect olfactory receptor OR5 from Machilis ... -

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Basic information

Entry
Database: PDB / ID: 7lig
TitleThe structure of the insect olfactory receptor OR5 from Machilis hrabei in complex with DEET
ComponentsMhOR5
KeywordsMEMBRANE PROTEIN / olfactory receptor / ion channel / DEET
Function / homologyN,N-diethyl-3-methylbenzamide
Function and homology information
Biological speciesMachilis hrabei (insect)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
Authorsdel Marmol, J. / Ruta, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nature / Year: 2021
Title: The structural basis of odorant recognition in insect olfactory receptors.
Authors: Josefina Del Mármol / Mackenzie A Yedlin / Vanessa Ruta /
Abstract: Olfactory systems must detect and discriminate amongst an enormous variety of odorants. To contend with this challenge, diverse species have converged on a common strategy in which odorant identity ...Olfactory systems must detect and discriminate amongst an enormous variety of odorants. To contend with this challenge, diverse species have converged on a common strategy in which odorant identity is encoded through the combinatorial activation of large families of olfactory receptors, thus allowing a finite number of receptors to detect a vast chemical world. Here we offer structural and mechanistic insight into how an individual olfactory receptor can flexibly recognize diverse odorants. We show that the olfactory receptor MhOR5 from the jumping bristletail Machilis hrabei assembles as a homotetrameric odorant-gated ion channel with broad chemical tuning. Using cryo-electron microscopy, we elucidated the structure of MhOR5 in multiple gating states, alone and in complex with two of its agonists-the odorant eugenol and the insect repellent DEET. Both ligands are recognized through distributed hydrophobic interactions within the same geometrically simple binding pocket located in the transmembrane region of each subunit, suggesting a structural logic for the promiscuous chemical sensitivity of this receptor. Mutation of individual residues lining the binding pocket predictably altered the sensitivity of MhOR5 to eugenol and DEET and broadly reconfigured the receptor's tuning. Together, our data support a model in which diverse odorants share the same structural determinants for binding, shedding light on the molecular recognition mechanisms that ultimately endow the olfactory system with its immense discriminatory capacity.
History
DepositionJan 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: 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 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: MhOR5
B: MhOR5
C: MhOR5
D: MhOR5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,7128
Polymers214,9474
Non-polymers7654
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "D"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "A"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPUNKG - H1
d_21ens_1ASPUNKC - D1
d_31ens_1ASPUNKE - F1
d_41ens_1ASPUNKA - B1

NCS oper:
IDCodeMatrixVector
1given(-0.999990210781, 0.00228215611873, 0.00379079222967), (-0.00228160361236, -0.999997385879, 0.0001500677467), (0.00379112479811, 0.000141417192409, 0.999992803661)110.753577153, 111.525214035, -0.391648768221
2given(0.00421562058575, 0.999991114149, -1.29006303689E-5), (-0.999988082134, 0.00421563957208, 0.0024625137284), (0.00246254623128, 2.51945305477E-6, 0.999996967925)-0.44162046331, 110.876323377, -0.206395079398
3given(0.00749533831622, -0.999965697167, -0.00352482510404), (0.999969850376, 0.00750242980542, -0.00200296923486), (0.00202934528026, -0.00350970589983, 0.999991781827)110.823305204, -0.274531189947, -0.00542385551344

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Components

#1: Protein
MhOR5


Mass: 53736.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Machilis hrabei (insect) / Production host: Homo sapiens (human)
#2: Chemical
ChemComp-DE3 / N,N-diethyl-3-methylbenzamide / DEET


Mass: 191.269 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H17NO / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homotetrameric olfactory receptor MhOR5 in complex with DEET
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Machilis hrabei (insect)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer componentConc.: 1 mM / Name: DEET
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.51 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18rc1_3777refinement
PHENIX1.18rc1_3777refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56191 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 59.08 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005212424
ELECTRON MICROSCOPYf_angle_d0.726716852
ELECTRON MICROSCOPYf_chiral_restr0.0442016
ELECTRON MICROSCOPYf_plane_restr0.00772020
ELECTRON MICROSCOPYf_dihedral_angle_d18.43721656
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000707272520178
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000713063335539
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000705971873224

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