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- EMDB-35971: Human Consensus Olfactory Receptor OR52c in apo state, OR52c-bRIL -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Human Consensus Olfactory Receptor OR52c in apo state, OR52c-bRIL | |||||||||
![]() | Global non-uniform refined map of apo-state OR52cs. | |||||||||
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![]() | Olfactory Receptor / G Protein / MEMBRANE PROTEIN / GPCR / Olfactory GPCR | |||||||||
Function / homology | Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding / Soluble cytochrome b562![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.66 Å | |||||||||
![]() | Choi CW / Bae J / Choi H-J / Kim J | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 61.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.3 KB 17.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 131.2 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 116 MB 116 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j46MC ![]() 8htgC ![]() 8htiC ![]() 8w77C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Global non-uniform refined map of apo-state OR52cs. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.848 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B of apo-state OR52cs.
File | emd_35971_half_map_1.map | ||||||||||||
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Annotation | Half map B of apo-state OR52cs. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of apo-state OR52cs.
File | emd_35971_half_map_2.map | ||||||||||||
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Annotation | Half map A of apo-state OR52cs. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab
Entire | Name: Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab |
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Components |
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-Supramolecule #1: Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab
Supramolecule | Name: Complex of Consensus Olfactory receptor OR52c and anti-bRIL Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 140 KDa |
-Macromolecule #1: Olfactory receptor OR52c,Soluble cytochrome b562
Macromolecule | Name: Olfactory receptor OR52c,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 49.480332 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11 | |||||||||||||||
Vitrification | Cryogen 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
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | ![]() PDB-8j46: |