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- EMDB-36708: Cryo-EM structure of BlCHR2 class one -

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Basic information

Entry
Database: EMDB / ID: EMD-36708
TitleCryo-EM structure of BlCHR2 class one
Map data
Sample
  • Complex: BlCHR2
    • Protein or peptide: BlCHR2
  • Ligand: POTASSIUM ION
  • Ligand: RETINAL
  • Ligand: water
Keywordschannelrhodopsin / MEMBRANE PROTEIN
Biological speciesBilabrum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZhang MF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of BlCHR2 class one
Authors: Zhang MF
History
DepositionJul 1, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36708.png

Downloads & links

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Map

FileDownload / File: emd_36708.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.35 Å/pix.
x 640 pix.
= 224. Å		0.35 Å/pix.
x 640 pix.
= 224. Å		0.35 Å/pix.
x 640 pix.
= 224. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.21794492 - 0.31115675
Average (Standard dev.)0.00009045395 (±0.009260478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 224.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36708_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_36708_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 : BlCHR2

EntireName: BlCHR2
Components
  • Complex: BlCHR2
    • Protein or peptide: BlCHR2
  • Ligand: POTASSIUM ION
  • Ligand: RETINAL
  • Ligand: water

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Supramolecule #1: BlCHR2

SupramoleculeName: BlCHR2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bilabrum (eukaryote)

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Macromolecule #1: BlCHR2

MacromoleculeName: BlCHR2 / type: protein_or_peptide / ID: 1 / Details: GB:OP710242 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bilabrum (eukaryote)
Molecular weightTheoretical: 43.984391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSECCELCVC QKEPGTFGAL IAVNTITAII LVAAGAYMAW KTAAGLGWNT RPHGPEGPPE ENWLSPGISI LCGVMYAFKA IDWASYNDT GESTAFSLNQ VWYSDYLITC PLLVLDFCIT VNLRYKLVFS SSIACLLAIA VSTFIVDAPY RYYMYGIGLA G FICAGYAL ...String:
MSECCELCVC QKEPGTFGAL IAVNTITAII LVAAGAYMAW KTAAGLGWNT RPHGPEGPPE ENWLSPGISI LCGVMYAFKA IDWASYNDT GESTAFSLNQ VWYSDYLITC PLLVLDFCIT VNLRYKLVFS SSIACLLAIA VSTFIVDAPY RYYMYGIGLA G FICAGYAL WNEINAQREK IPDSAWWYLS AGRLIFFAGW PFFPLLWTLS FHTSGVINEE WYFILHAILD ILCKAVFGFF ML GFRLELE ELDFKAIEAE QAKLEGDKEA QALKNDKDTG EVLRHYNRAS SGFFGQGIPD DQGSVSGGSV LMSRARRQHM LYR REASYL SMDPMAEKIR ELEMLKKKIQ KEVDSRSKKM QREMTARFAI QDDSDDEDGG RGAGSARRRK NARRG

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 18 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #3: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 3 / Number of copies: 3 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 9 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40700
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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