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- EMDB-42945: AgamOR28 structure without ligand -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-42945
TitleAgamOR28 structure without ligand
Map data
Sample
  • Complex: AgamOR28 heterotetramer without ligand
    • Complex: Anopheles gambiae OR28
      • Protein or peptide: OR28
    • Complex: Apocrypta bakeri Orco
      • Protein or peptide: Odorant receptor Orco
KeywordsMosquitoes / Olfaction / Channel / Heterotetramer / MEMBRANE PROTEIN
Function / homology
Function and homology information


olfactory receptor activity / detection of chemical stimulus involved in sensory perception of smell / 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
Uncharacterized protein / Odorant receptor
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito) / Apocrypta bakeri (insect)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 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 27, 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_42945.png

Downloads & links

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Map

FileDownload / File: emd_42945.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.64 Å		1.06 Å/pix.
x 240 pix.
= 254.64 Å		1.06 Å/pix.
x 240 pix.
= 254.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.0.8250.8250.825
CCP4 map header1.0611.0611.061
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.6843116 - 1.0407991
Average (Standard dev.)0.0004325921 (±0.026473414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 237.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_42945_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_42945_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 : AgamOR28 heterotetramer without ligand

EntireName: AgamOR28 heterotetramer without ligand
Components
  • Complex: AgamOR28 heterotetramer without ligand
    • Complex: Anopheles gambiae OR28
      • Protein or peptide: OR28
    • Complex: Apocrypta bakeri Orco
      • Protein or peptide: Odorant receptor Orco

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Supramolecule #1: AgamOR28 heterotetramer without ligand

SupramoleculeName: AgamOR28 heterotetramer without ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Anopheles gambiae OR28

SupramoleculeName: Anopheles gambiae OR28 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Anopheles gambiae (African malaria 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: OR28

MacromoleculeName: OR28 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Anopheles gambiae (African malaria mosquito)
Molecular weightTheoretical: 45.826898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARLVLHEVR YVLMAMLYIS RGMAKQIQNS TIDLYVYWFL TFIPIASLCV PQFTYLVVDT KSLIDFISVL VPITEILLTN GKMIICNVK RGKIINLINQ VQVAWDECAK SEHLEIQTLI TATAKKTKIF VIIYTTSFLL ICVEYSSMPL FKLIYHSAVY G KQSNYTIA ...String:
MARLVLHEVR YVLMAMLYIS RGMAKQIQNS TIDLYVYWFL TFIPIASLCV PQFTYLVVDT KSLIDFISVL VPITEILLTN GKMIICNVK RGKIINLINQ VQVAWDECAK SEHLEIQTLI TATAKKTKIF VIIYTTSFLL ICVEYSSMPL FKLIYHSAVY G KQSNYTIA LPYLSRFAYS TESTTSFAWT YFFILLGVYL LALTLSGFDS LFATLVMHVK MMFKVLKFEI EQLGLDLSAG KS HVELQAK LKQIILKHKT NLSLIEQLED GFSFFLMAQF LTSSILVCVV LYELTMVFGW NEDTFKTVTY LPGAILQLFL FCW YAQQIT EEARLVSDHI YNIPWYLADP KLQKDILTFM VKAQKPTGVT ASKFYMVTLQ TFQRISSTSY SYFTLLQTIN QQ

UniProtKB: Uncharacterized protein

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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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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 recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 377441
FSC plot (resolution estimation)

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