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- PDB-8j46: Human Consensus Olfactory Receptor OR52c in apo state, OR52c-bRIL -

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Basic information

Entry
Database: PDB / ID: 8j46
TitleHuman Consensus Olfactory Receptor OR52c in apo state, OR52c-bRIL
ComponentsOlfactory receptor OR52c,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / Olfactory Receptor / G Protein / GPCR / Olfactory GPCR
Function / homologyCytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding / Soluble cytochrome b562
Function and homology information
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsChoi, C.W. / Bae, J. / Choi, H.-J. / Kim, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Samsung Science and Technology FoundationSSTF-BA1901-09 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2023
Title: Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family.
Authors: Chulwon Choi / Jungnam Bae / Seonghan Kim / Seho Lee / Hyunook Kang / Jinuk Kim / Injin Bang / Kiheon Kim / Won-Ki Huh / Chaok Seok / Hahnbeom Park / Wonpil Im / Hee-Jung Choi /
Abstract: Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of ...Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of OR51E2 bound to propionate provided molecular insight into odorant recognition, but the lack of an inactive OR structure limited understanding of the activation mechanism of ORs upon odorant binding. Here, we determined the cryo-electron microscopy structures of consensus OR52 (OR52), a representative of the OR52 family, in the ligand-free (apo) and octanoate-bound states. The apo structure of OR52 reveals a large opening between transmembrane helices (TMs) 5 and 6. A comparison between the apo and active structures of OR52 demonstrates the inward and outward movements of the extracellular and intracellular segments of TM6, respectively. These results, combined with molecular dynamics simulations and signaling assays, shed light on the molecular mechanisms of odorant binding and activation of the OR52 family.
History
DepositionApr 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Olfactory receptor OR52c,Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)49,4801
Polymers49,4801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Olfactory receptor OR52c,Soluble cytochrome b562


Mass: 49480.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7
Has protein modificationY

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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: Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.14 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Escherichia coli (E. coli)562
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf9
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris(hydroxymethyl)aminomethaneNH2C(CH2OH)31
2100 mMSodium ChlorideNaCl1
30.005 %Lauryl Maltose Neopentyl GlycolC47H88O221
40.0005 %Cholesteryl hemisuccinateC31H50O41
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: blot time 3 seconds

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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 FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1900 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 68.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.0particle selection
4cryoSPARC4.2.0CTF correction
10cryoSPARC4.2.0initial Euler assignment
11cryoSPARC4.2.0final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173732 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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