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- EMDB-35423: HcCCR in NaCl -

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Basic information

Entry
Database: EMDB / ID: EMD-35423
TitleHcCCR in NaCl
Map data
Sample
  • Complex: HcCCR
    • Protein or peptide: HcCCR
  • Ligand: RETINAL
  • Ligand: SODIUM ION
  • Ligand: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: water
Keywordschannelrhodopsin / MEMBRANE PROTEIN
Biological speciesHyphochytrium catenoides (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsZhang MF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of HcCCR
Authors: Zhang MF
History
DepositionFeb 19, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35423.png

Downloads & links

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Map

FileDownload / File: emd_35423.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 480 pix.
= 273.6 Å		0.57 Å/pix.
x 480 pix.
= 273.6 Å		0.57 Å/pix.
x 480 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.8154063 - 1.2305285
Average (Standard dev.)-0.00034104526 (±0.029293137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35423_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_35423_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 : HcCCR

EntireName: HcCCR
Components
  • Complex: HcCCR
    • Protein or peptide: HcCCR
  • Ligand: RETINAL
  • Ligand: SODIUM ION
  • Ligand: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: water

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Supramolecule #1: HcCCR

SupramoleculeName: HcCCR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Hyphochytrium catenoides (eukaryote)

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Macromolecule #1: HcCCR

MacromoleculeName: HcCCR / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Hyphochytrium catenoides (eukaryote)
Molecular weightTheoretical: 30.224213 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPFCGGRPED GWHHGSIHDM DYPLLGAMAA ICSVFIGGSG AWMLYRLDLG LGYSCKPHHS GYAPEANSFS ALSCLVSGTI YAAKTFDFF DGGGTPFSFN WYWYLDYVFT CPLILLDVLY TLEIPHKLRF VFAVIITLWC GVAAFVTPSA FRFGYYAVGC V WFVPFSFS ...String:
MPFCGGRPED GWHHGSIHDM DYPLLGAMAA ICSVFIGGSG AWMLYRLDLG LGYSCKPHHS GYAPEANSFS ALSCLVSGTI YAAKTFDFF DGGGTPFSFN WYWYLDYVFT CPLILLDVLY TLEIPHKLRF VFAVIITLWC GVAAFVTPSA FRFGYYAVGC V WFVPFSFS LLRHVKQRYQ VYPPKCQKIL FWACTIFFGF WPLFPILFLF SWLGTGHIDQ QAFTIIHAFL DLFCKTVFGL IM TFFRLEL EEHTEVLGLP LNEPKGKH

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Macromolecule #2: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 2 / Number of copies: 3 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 48
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadeca...

MacromoleculeName: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
type: ligand / ID: 4 / Number of copies: 6 / Formula: L9Q
Molecular weightTheoretical: 746.05 Da
Chemical component information

ChemComp-L9Q:
(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 33 / 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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 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: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 267000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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