[English] 日本語
Yorodumi- EMDB-39858: Cryo-EM structure of the insect olfactory receptor OR5-Orco heter... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39858 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the insect olfactory receptor OR5-Orco heterocomplex from Acyrthosiphon pisum bound with geranyl acetate | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | MEMBRANE PROTEIN | |||||||||
Function / homology | Olfactory receptor, insect / 7tm Odorant receptor / olfactory receptor activity / odorant binding / signal transduction / plasma membrane / Odorant receptor / Odorant receptor Function and homology information | |||||||||
Biological species | Acyrthosiphon pisum (pea aphid) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Wang YD / Qiu L / Guan ZY / Wang Q / Wang GR / Yin P | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: Science / Year: 2024 Title: Structural basis for odorant recognition of the insect odorant receptor OR-Orco heterocomplex. Authors: Yidong Wang / Liang Qiu / Bing Wang / Zeyuan Guan / Zhi Dong / Jie Zhang / Song Cao / Lulu Yang / Bo Wang / Zhou Gong / Liwei Zhang / Weihua Ma / Zhu Liu / Delin Zhang / Guirong Wang / Ping Yin / Abstract: Insects detect and discriminate a diverse array of chemicals using odorant receptors (ORs), which are ligand-gated ion channels comprising a divergent odorant-sensing OR and a conserved odorant ...Insects detect and discriminate a diverse array of chemicals using odorant receptors (ORs), which are ligand-gated ion channels comprising a divergent odorant-sensing OR and a conserved odorant receptor co-receptor (Orco). In this work, we report structures of the OR5-Orco heterocomplex from the pea aphid alone and bound to its known activating ligand, geranyl acetate. In these structures, three Orco subunits serve as scaffold components that cannot bind the ligand and remain relatively unchanged. Upon ligand binding, the pore-forming helix S7b of OR5 shifts outward from the central pore axis, causing an asymmetrical pore opening for ion influx. Our study provides insights into odorant recognition and channel gating of the OR-Orco heterocomplex and offers structural resources to support development of innovative insecticides and repellents for pest control. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_39858.map.gz | 49.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-39858-v30.xml emd-39858.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
Images | emd_39858.png | 45.1 KB | ||
Filedesc metadata | emd-39858.cif.gz | 5.9 KB | ||
Others | emd_39858_half_map_1.map.gz emd_39858_half_map_2.map.gz | 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39858 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39858 | HTTPS FTP |
-Validation report
Summary document | emd_39858_validation.pdf.gz | 806 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_39858_full_validation.pdf.gz | 805.5 KB | Display | |
Data in XML | emd_39858_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_39858_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39858 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39858 | HTTPS FTP |
-Related structure data
Related structure data | 8z9aMC 8z9zC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_39858.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #1
File | emd_39858_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_39858_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : OR-Orco heterocomplex
Entire | Name: OR-Orco heterocomplex |
---|---|
Components |
|
-Supramolecule #1: OR-Orco heterocomplex
Supramolecule | Name: OR-Orco heterocomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: Acyrthosiphon pisum (pea aphid) |
-Macromolecule #1: Odorant receptor, ApisOrco
Macromolecule | Name: Odorant receptor, ApisOrco / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Acyrthosiphon pisum (pea aphid) |
Molecular weight | Theoretical: 52.916766 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGYKKDGLIK DLWPNIRLIQ LSGLFISEYY DDYSGLAVLF RKIYSWITAI IIYSQFIFIV IFMVTKSNDS DQLAAGVVTT LFFTHSMIK FVYFSTGTKS FYRTLSCWNN TSPHPLFAES HSRFHAKSLS RMRQLLIIVS IVTIFTTISW TTITFFGESV W KVPDPETF ...String: MGYKKDGLIK DLWPNIRLIQ LSGLFISEYY DDYSGLAVLF RKIYSWITAI IIYSQFIFIV IFMVTKSNDS DQLAAGVVTT LFFTHSMIK FVYFSTGTKS FYRTLSCWNN TSPHPLFAES HSRFHAKSLS RMRQLLIIVS IVTIFTTISW TTITFFGESV W KVPDPETF NQTMYVPVPR LMLHSWYPWD SGHGLGYIVA FVLQFYWVFI TLSHSNLMEL LFSSFLVHAC EQLQHLKEIL NP LIELSAT LDSSVHNPAE IFRANSAKNQ SINGIDHDYN GSYVNEITEY GTKGENEPNR KGPNNLTSNQ EVLVRSAIKY WVE RHKHVV KYVSLITECY GSALLFHMLV STVILTILAY QATKINGVNV FAFSTIGYLM YSFAQIFMFC IHGNELIEES SSVM EAAYG CHWYDGSEEA KTFVQIVCQQ CQKPLIVSGA KFFNVSLDLF ASVLGAVVTY FMVLVQLK UniProtKB: Odorant receptor |
-Macromolecule #2: Odorant receptor, ApisOR5
Macromolecule | Name: Odorant receptor, ApisOR5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Acyrthosiphon pisum (pea aphid) |
Molecular weight | Theoretical: 42.45407 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MQRIDTINMF LQMTGCTDSK AMLYLTYFEF LITFYYLIAT YASIVHFEQS VTIQLFALLC MLIECVILLN ITFRLYHKNH IREMHQYSR RLGIPDSYRS VINVITKYHL IASNIFVVFP VTYAIFCDSV RVGDPFTFPF LDVLPMHTDN LAIYACKYLV Y AISVYIAH ...String: MQRIDTINMF LQMTGCTDSK AMLYLTYFEF LITFYYLIAT YASIVHFEQS VTIQLFALLC MLIECVILLN ITFRLYHKNH IREMHQYSR RLGIPDSYRS VINVITKYHL IASNIFVVFP VTYAIFCDSV RVGDPFTFPF LDVLPMHTDN LAIYACKYLV Y AISVYIAH VELCFINTTF IYYVGVLKHR LETIVQTIGE AFADNDEQKF KYAIIQHQKL LSYFNTMKIV FSKPILLSMS FN AIYFGLT TSFVIQAIRG YINQAILSIC IASSAAAVIN ITIYTFYGSE LMDLHDKILH VLFDNAFFYV SKSFKSSILI MMT RVTIPL KFTVGYIFTI NLNLLLKILK MSYTVLNVLL SSETIKPHKL S UniProtKB: Odorant receptor |
-Macromolecule #3: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 7 / Formula: PC1 |
---|---|
Molecular weight | Theoretical: 790.145 Da |
Chemical component information | ChemComp-PC1: |
-Macromolecule #4: [(2E)-3,7-dimethylocta-2,6-dienyl] ethanoate
Macromolecule | Name: [(2E)-3,7-dimethylocta-2,6-dienyl] ethanoate / type: ligand / ID: 4 / Number of copies: 1 / Formula: SOU |
---|---|
Molecular weight | Theoretical: 196.286 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7.5 mg/mL |
---|---|
Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 399858 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |