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- EMDB-42850: AaegOR10 structure bound to o-cresol -

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Basic information

Entry
Database: EMDB / ID: EMD-42850
TitleAaegOR10 structure bound to o-cresol
Map data
Sample
  • Complex: AaegOR10 heterotetramer bound to o-cresol
    • Complex: Aedes aegypti OR10
      • Protein or peptide: Odorant receptor OR10
    • Complex: Apocrypta bakeri Orco
      • Protein or peptide: Odorant receptor Orco
  • Ligand: o-cresol
KeywordsMosquito olfactory receptor OR10 / MEMBRANE PROTEIN
Function / homology
Function and homology information


olfactory receptor activity / odorant binding / membrane => GO:0016020 / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Olfactory receptor, insect / 7tm Odorant receptor
Similarity search - Domain/homology
Odorant receptor / Odorant receptor
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito) / Apocrypta bakeri (insect)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhao J / del Marmol J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)5R00DC019401 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2024
Title: Structural basis of odor sensing by insect heteromeric odorant receptors
Authors: Zhao J / Chen AQ / Ryu J / del Marmol J
History
DepositionNov 16, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42850.png

Downloads & links

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Map

FileDownload / File: emd_42850.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 330 pix.
= 273.9 Å		0.83 Å/pix.
x 330 pix.
= 273.9 Å		0.83 Å/pix.
x 330 pix.
= 273.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.1482375 - 1.5733052
Average (Standard dev.)0.000025983181 (±0.031006062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 273.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_42850_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42850_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AaegOR10 heterotetramer bound to o-cresol

EntireName: AaegOR10 heterotetramer bound to o-cresol
Components
  • Complex: AaegOR10 heterotetramer bound to o-cresol
    • Complex: Aedes aegypti OR10
      • Protein or peptide: Odorant receptor OR10
    • Complex: Apocrypta bakeri Orco
      • Protein or peptide: Odorant receptor Orco
  • Ligand: o-cresol

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Supramolecule #1: AaegOR10 heterotetramer bound to o-cresol

SupramoleculeName: AaegOR10 heterotetramer bound to o-cresol / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Aedes aegypti OR10

SupramoleculeName: Aedes aegypti OR10 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Aedes aegypti (yellow fever mosquito)

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Supramolecule #3: Apocrypta bakeri Orco

SupramoleculeName: Apocrypta bakeri Orco / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Apocrypta bakeri (insect)

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Macromolecule #1: Odorant receptor OR10

MacromoleculeName: Odorant receptor OR10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aedes aegypti (yellow fever mosquito)
Molecular weightTheoretical: 43.491168 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASILDCPIV SVNARVWRFW SFVLKHDAMR YISIIPVTVM TFFMFTDLCR SWGNIQELII KAYFAVLYFN AVLRTLILVK DRKLYENFM QGISNVYFEI SHIDDHKIQS LLKSYTVRAR MLSISNLALG AIISTCFVVY PIFTGERGLP YGMFIPGLDS F RSPHYEII ...String:
MASILDCPIV SVNARVWRFW SFVLKHDAMR YISIIPVTVM TFFMFTDLCR SWGNIQELII KAYFAVLYFN AVLRTLILVK DRKLYENFM QGISNVYFEI SHIDDHKIQS LLKSYTVRAR MLSISNLALG AIISTCFVVY PIFTGERGLP YGMFIPGLDS F RSPHYEII YIVQVVLTFP GCCMYIPFTS FFASTTLFGL VQIKTLQRQL QTFKDNINSQ DKEKVKAKVV KLIEDHKRII TY VSELNSL VTYICFVEFL SFGMMLCALL FLLNVIENHA QIVIVAAYIF MIISQIFAFY WHANEVREES MNLAEAAYSG PWV ELDNSI KKKLLLIILR AQQPLEITVG NVYPMTLEMF QSLLNASYSY FTLLRRVYN

UniProtKB: Odorant receptor

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Macromolecule #2: Odorant receptor Orco

MacromoleculeName: Odorant receptor Orco / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Apocrypta bakeri (insect)
Molecular weightTheoretical: 53.204953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKFKHQGLVA DLLPNIRVMQ GVGHFMFNYY SEGKKFPHRI YCIVTLLLLL LQYGMMAVNL MMESDDVDDL TANTITMLFF LHPIVKMIY FPVRSKIFYK TLAIWNNPNS HPLFAESNAR FHALAITKMR RLLFCVAGAT IFSVISWTGI TFIEDSVKRI T DPETNETT ...String:
MKFKHQGLVA DLLPNIRVMQ GVGHFMFNYY SEGKKFPHRI YCIVTLLLLL LQYGMMAVNL MMESDDVDDL TANTITMLFF LHPIVKMIY FPVRSKIFYK TLAIWNNPNS HPLFAESNAR FHALAITKMR RLLFCVAGAT IFSVISWTGI TFIEDSVKRI T DPETNETT IIPIPRLMIR TFYPFNAMSG AGHVFALIYQ FYYLVISMAV SNSLDVLFCS WLLFACEQLQ HLKAIMKPLM EL SATLDTV VPNSGELFKA GSADHLRESQ GVQPSGNGDN VLDVDLRGIY SNRQDFTATF RPTAGTTFNG GVGPNGLTKK QEM LVRSAI KYWVERHKHV VRLVTAVGDA YGVALLLHML TTTITLTLLA YQATKVNGVN VYAATVIGYL LYTLGQVFLF CIFG NRLIE ESSSVMEAAY SCHWYDGSEE AKTFVQIVCQ QCQKAMSISG AKFFTVSLDL FASVLGAVVT YFMVLVQLK

UniProtKB: Odorant receptor

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Macromolecule #3: o-cresol

MacromoleculeName: o-cresol / type: ligand / ID: 3 / Number of copies: 1 / Formula: JZ0
Molecular weightTheoretical: 108.138 Da
Chemical component information

ChemComp-JZ0:
o-cresol / O-Cresol

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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: 2.0 µm / Nominal defocus min: 1.0 µm
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Average electron dose: 55.2 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 58.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model generated in cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 496871
Image recording ID1
FSC plot (resolution estimation)

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