[English] 日本語
Yorodumi
- EMDB-7352: Cryo-EM structure of Orco -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7352
TitleCryo-EM structure of Orco
Map dataOdorant receptor
Sample
  • Complex: Orco homotetramer bound to four Fab molecules in a detergent micelle
    • Protein or peptide: Odorant receptor
KeywordsOlfactory receptor / Ion channel / Insect / Fab / MEMBRANE PROTEIN
Function / homologyOlfactory receptor, insect / 7tm Odorant receptor / olfactory receptor activity / odorant binding / signal transduction / identical protein binding / plasma membrane / Odorant receptor
Function and homology information
Biological speciesApocrypta bakeri (insect)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsButterwick JA / Kim KH / Walz T / Ruta V
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI103171 United States
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of the insect olfactory receptor Orco.
Authors: Joel A Butterwick / Josefina Del Mármol / Kelly H Kim / Martha A Kahlson / Jackson A Rogow / Thomas Walz / Vanessa Ruta /
Abstract: The olfactory system must recognize and discriminate amongst an enormous variety of chemicals in the environment. To contend with such diversity, insects have evolved a family of odorant-gated ion ...The olfactory system must recognize and discriminate amongst an enormous variety of chemicals in the environment. To contend with such diversity, insects have evolved a family of odorant-gated ion channels comprised of a highly conserved co-receptor (Orco) and a divergent odorant receptor (OR) that confers chemical specificity. Here, we present the single-particle cryo-electron microscopy structure of an Orco homomer from the parasitic fig wasp Apocrypta bakeri at 3.5 Å resolution, providing structural insight into this receptor family. Orco possesses a novel channel architecture, with four subunits symmetrically arranged around a central pore that diverges into four lateral conduits that open to the cytosol. The Orco tetramer has few inter-subunit interactions within the membrane and is bound together by a small cytoplasmic anchor domain. The minimal sequence conservation among ORs maps largely to the pore and anchor domain, shedding light on how the architecture of this receptor family accommodates its remarkable sequence diversity and facilitates the evolution of odour tuning.
History
DepositionJan 19, 2018-
Header (metadata) releaseMar 21, 2018-
Map releaseAug 22, 2018-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6c70
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7352.png

Downloads & links

-
Map

FileDownload / File: emd_7352.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOdorant receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 384 pix.
= 384. Å		1 Å/pix.
x 384 pix.
= 384. Å		1 Å/pix.
x 384 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0 / Movie #1: 8
Minimum - Maximum-9.285572 - 18.670680000000001
Average (Standard dev.)-0.15935563 (±0.6412915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z384.000384.000384.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-9.28618.671-0.159

-
Supplemental data

-
Sample components

-
Entire : Orco homotetramer bound to four Fab molecules in a detergent micelle

EntireName: Orco homotetramer bound to four Fab molecules in a detergent micelle
Components
  • Complex: Orco homotetramer bound to four Fab molecules in a detergent micelle
    • Protein or peptide: Odorant receptor

-
Supramolecule #1: Orco homotetramer bound to four Fab molecules in a detergent micelle

SupramoleculeName: Orco homotetramer bound to four Fab molecules in a detergent micelle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Apocrypta bakeri (insect)

-
Macromolecule #1: Odorant receptor

MacromoleculeName: Odorant receptor / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Apocrypta bakeri (insect)
Molecular weightTheoretical: 53.513238 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGRAKFKHQ GLVADLLPNI RVMQGVGHFM FNYYSEGKKF PHRIYCIVTL LLLLLQYGMM AVNLMMESDD VDDLTANTIT MLFFLHPIV KMIYFPVRSK IFYKTLAIWN NPNSHPLFAE SNARFHALAI TKMRRLLFCV AGATIFSVIS WTGITFIEDS V KRITDPET ...String:
GPGRAKFKHQ GLVADLLPNI RVMQGVGHFM FNYYSEGKKF PHRIYCIVTL LLLLLQYGMM AVNLMMESDD VDDLTANTIT MLFFLHPIV KMIYFPVRSK IFYKTLAIWN NPNSHPLFAE SNARFHALAI TKMRRLLFCV AGATIFSVIS WTGITFIEDS V KRITDPET NETTIIPIPR LMIRTFYPFN AMSGAGHVFA LIYQFYYLVI SMAVSNSLDV LFCSWLLFAC EQLQHLKAIM KP LMELSAT LDTVVPNSGE LFKAGSADHL RESQGVQPSG NGDNVLDVDL RGIYSNRQDF TATFRPTAGT TFNGGVGPNG LTK KQEMLV RSAIKYWVER HKHVVRLVTA VGDAYGVALL LHMLTTTITL TLLAYQATKV NGVNVYAATV IGYLLYTLGQ VFLF CIFGN RLIEESSSVM EAAYSCHWYD GSEEAKTFVQ IVCQQCQKAM SISGAKFFTV SLDLFASVLG AVVTYFMVLV QLK

UniProtKB: Odorant receptor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 1221 / Number real images: 53141 / Average exposure time: 0.2 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53141
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
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