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- EMDB-72977: Octopus sensory receptor CRT1 bound to Progesterone -

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Basic information

Entry
Database: EMDB / ID: EMD-72977
TitleOctopus sensory receptor CRT1 bound to Progesterone
Map data
Sample
  • Complex: octopus chemotactile receptor CRT1 bound to progesterone
    • Protein or peptide: Chemotactile receptor CRT1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PROGESTERONE
Keywordscomplex / membrane protein
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Chemotactile receptor for terpenes 1
Similarity search - Component
Biological speciesOctopus bimaculoides (California two-spot octopus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsJiang H / Hibbs RE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: To Be Published
Title: A sensory system for mating in octopus
Authors: Villar PS / Jiang H / Shugaeva T / Berdan EL / Kulkarni A / Hiroi M / Masucci G / Reiter S / Lindahl E / Howard RJ / Hibbs RE / Bellono NW
History
DepositionOct 1, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72977.png

Downloads & links

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Map

FileDownload / File: emd_72977.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.21168788 - 0.611191
Average (Standard dev.)0.0012126708 (±0.015254051)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72977_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72977_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72977_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 : octopus chemotactile receptor CRT1 bound to progesterone

EntireName: octopus chemotactile receptor CRT1 bound to progesterone
Components
  • Complex: octopus chemotactile receptor CRT1 bound to progesterone
    • Protein or peptide: Chemotactile receptor CRT1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PROGESTERONE

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Supramolecule #1: octopus chemotactile receptor CRT1 bound to progesterone

SupramoleculeName: octopus chemotactile receptor CRT1 bound to progesterone
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Octopus bimaculoides (California two-spot octopus)

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Macromolecule #1: Chemotactile receptor CRT1

MacromoleculeName: Chemotactile receptor CRT1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Octopus bimaculoides (California two-spot octopus)
Molecular weightTheoretical: 47.334262 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIFVIYLVFI LISSIPIVKS TPTYGDERLL REKLLTNYSK SIRPVINLTK VVDVTALLYL QTLYDLDFVN NFIMARYYLG LIWIDEKLT WNPLDYNNIT SIYLPKDKIW TPPIKMCNSM DKSEENDGVG ELMLTYTGWI NMWSFRLLHT YCQINAYTYP F DEHTCEIY ...String:
MIFVIYLVFI LISSIPIVKS TPTYGDERLL REKLLTNYSK SIRPVINLTK VVDVTALLYL QTLYDLDFVN NFIMARYYLG LIWIDEKLT WNPLDYNNIT SIYLPKDKIW TPPIKMCNSM DKSEENDGVG ELMLTYTGWI NMWSFRLLHT YCQINAYTYP F DEHTCEIY LCVALHTINH TRIKELIYED SKFTQNYKWD INVSGKVNGT DELFSYAFAP MYLRRKLTVG IIAMLIPTVM MT ILTIFVF LLPPESGEKV SLATTIFLSN VLYLVQIDKT TPTNTKYPSL LMLYLMLLSM LSGIATLGSV VISKLYVIQS PSL RKSNPS DQNMNKSHTN KVADISTISK VQSDLPIREK PNEKRIYCIS DYIRLDDIFL KLSIATSVII SMIFTCLLFI PLES SAWSH PQFEK

UniProtKB: Chemotactile receptor for terpenes 1

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 25 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: PROGESTERONE

MacromoleculeName: PROGESTERONE / type: ligand / ID: 3 / Number of copies: 5 / Formula: STR
Molecular weightTheoretical: 314.462 Da
Chemical component information

ChemComp-STR:
PROGESTERONE / hormone*YM

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8eis

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 241406
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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