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- EMDB-35971: Human Consensus Olfactory Receptor OR52c in apo state, OR52c-bRIL -

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Basic information

Entry
Database: EMDB / ID: EMD-35971
TitleHuman Consensus Olfactory Receptor OR52c in apo state, OR52c-bRIL
Map dataGlobal non-uniform refined map of apo-state OR52cs.
Sample
  • Complex: Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab
    • Protein or peptide: Olfactory receptor OR52c,Soluble cytochrome b562
KeywordsOlfactory Receptor / G Protein / MEMBRANE 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsChoi CW / Bae J / Choi H-J / Kim J
Funding support Korea, Republic Of, 1 items
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, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35971.png

Downloads & links

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Map

FileDownload / File: emd_35971.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal non-uniform refined map of apo-state OR52cs.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 271.36 Å		0.85 Å/pix.
x 320 pix.
= 271.36 Å		0.85 Å/pix.
x 320 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.2668895 - 0.4931219
Average (Standard dev.)-0.0006831258 (±0.010173134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B of apo-state OR52cs.

Fileemd_35971_half_map_1.map
AnnotationHalf map B of apo-state OR52cs.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of apo-state OR52cs.

Fileemd_35971_half_map_2.map
AnnotationHalf map A of apo-state OR52cs.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab

EntireName: Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab
Components
  • Complex: Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab
    • Protein or peptide: Olfactory receptor OR52c,Soluble cytochrome b562

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Supramolecule #1: Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab

SupramoleculeName: Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: Olfactory receptor OR52c,Soluble cytochrome b562

MacromoleculeName: Olfactory receptor OR52c,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.480332 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAID MPTSNHTSFH PSSFLLVGIP GLESVHIWIS IPFCAMYLIA LLGNSTLLFV IKTERSLHEP MYYFLAMLAA TDLVLSTST IPKMLAIFWF NLKEISFDAC LTQMFFIHSF TGMESGVLLA MAFDRYVAIC YPLRYTTILT NKVIGKIGMA V VLRAVLLV ...String:
DYKDDDDAID MPTSNHTSFH PSSFLLVGIP GLESVHIWIS IPFCAMYLIA LLGNSTLLFV IKTERSLHEP MYYFLAMLAA TDLVLSTST IPKMLAIFWF NLKEISFDAC LTQMFFIHSF TGMESGVLLA MAFDRYVAIC YPLRYTTILT NKVIGKIGMA V VLRAVLLV IPFPFLLKRL PFCGTNIIPH TYCEHMGVAK LACADIKVNI IYGLFVALLI VGLDVILIAL SYVLILRAAR RQ LADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGFD ILVGQIDDAL KLA NEGKVK EAQAAAEQLK TTRNAYIQKY LERARSTLLK ALSTCGSHIC VILAFYTPAF FSFLTHRFGH HIPPYIHILL ANLY LLVPP MLNPIIYGVK TKQIRERVLK IFFKKKASGL EVLFQ

UniProtKB: Soluble cytochrome b562

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3Tris(hydroxymethyl)aminomethane
100.0 mMNaClSodium Chloride
0.005 %C47H88O22Lauryl Maltose Neopentyl Glycol
0.0005 %C31H50O4Cholesteryl hemisuccinate
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 3 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 68.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Initial 3D model was generated with Ab-initio Reconstruction tool in cryoSPARC software.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 173732
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

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

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