[English] 日本語
Yorodumi
- EMDB-39858: Cryo-EM structure of the insect olfactory receptor OR5-Orco heter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39858
TitleCryo-EM structure of the insect olfactory receptor OR5-Orco heterocomplex from Acyrthosiphon pisum bound with geranyl acetate
Map data
Sample
  • Complex: OR-Orco heterocomplex
    • Protein or peptide: Odorant receptor, ApisOrco
    • Protein or peptide: Odorant receptor, ApisOR5
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: [(2E)-3,7-dimethylocta-2,6-dienyl] ethanoate
KeywordsMEMBRANE PROTEIN
Function / homologyOlfactory receptor, insect / 7tm Odorant receptor / olfactory receptor activity / odorant binding / signal transduction / plasma membrane / Odorant receptor / Odorant receptor
Function and homology information
Biological speciesAcyrthosiphon pisum (pea aphid)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWang YD / Qiu L / Guan ZY / Wang Q / Wang GR / Yin P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2024
Title: Structural basis for ligand modulation of insect olfactory receptor OR-Orco heterocomplex
Authors: Wang YD / Yin P
History
DepositionApr 23, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_39858.png

Downloads & links

-
Map

FileDownload / File: emd_39858.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-2.6173956 - 4.87328
Average (Standard dev.)0.0067998795 (±0.1287799)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_39858_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_39858_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : OR-Orco heterocomplex

EntireName: OR-Orco heterocomplex
Components
  • Complex: OR-Orco heterocomplex
    • Protein or peptide: Odorant receptor, ApisOrco
    • Protein or peptide: Odorant receptor, ApisOR5
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: [(2E)-3,7-dimethylocta-2,6-dienyl] ethanoate

-
Supramolecule #1: OR-Orco heterocomplex

SupramoleculeName: 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

MacromoleculeName: Odorant receptor, ApisOrco / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acyrthosiphon pisum (pea aphid)
Molecular weightTheoretical: 52.916766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

MacromoleculeName: Odorant receptor, ApisOR5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acyrthosiphon pisum (pea aphid)
Molecular weightTheoretical: 42.45407 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 7 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

-
Macromolecule #4: [(2E)-3,7-dimethylocta-2,6-dienyl] ethanoate

MacromoleculeName: [(2E)-3,7-dimethylocta-2,6-dienyl] ethanoate / type: ligand / ID: 4 / Number of copies: 1 / Formula: SOU
Molecular weightTheoretical: 196.286 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration7.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 399858

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more