+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34531 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Membrane protein BBiological membrane | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
| ||||||||||||||||||||||||
Keywords | Membrane Protein / Cryo-EM | ||||||||||||||||||||||||
Biological species | Hyphochytrium catenoides (eukaryote) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.53 Å | ||||||||||||||||||||||||
Authors | Tajima S / Kim Y / Yamashita K / Fukuda M / Deisseroth K / Kato HE | ||||||||||||||||||||||||
Funding support | Japan, 7 items
| ||||||||||||||||||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2023 Title: Structural basis for ion selectivity in potassium-selective channelrhodopsins Authors: Tajima S / Kim YS / Fukuda M / Jo Y / Wang PY / Paggi JM / Inoue M / Byrne EFX / Kishi KE / Nakamura S / Ramakrishnan C / Takaramoto S / Nagata T / Konno M / Sugiura M / Katayama K / Matsui ...Authors: Tajima S / Kim YS / Fukuda M / Jo Y / Wang PY / Paggi JM / Inoue M / Byrne EFX / Kishi KE / Nakamura S / Ramakrishnan C / Takaramoto S / Nagata T / Konno M / Sugiura M / Katayama K / Matsui TE / Yamashita K / Kim S / Ikeda H / Kim J / Kandori H / Dror RO / Inoue K / Deisseroth K / Kato HE | ||||||||||||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_34531.map.gz | 17.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-34531-v30.xml emd-34531.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34531_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_34531.png | 190.9 KB | ||
Masks | emd_34531_msk_1.map | 18.7 MB | Mask map | |
Others | emd_34531_additional_1.map.gz emd_34531_half_map_1.map.gz emd_34531_half_map_2.map.gz | 16.7 MB 17.3 MB 17.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34531 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34531 | HTTPS FTP |
-Related structure data
Related structure data | 8h87MC 8h86C 8iu0C M: atomic model generated by this map C: citing same article (ref.) |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_34531.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_34531_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: #1
File | emd_34531_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_34531_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_34531_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : HcKCR2
Entire | Name: HcKCR2 |
---|---|
Components |
|
-Supramolecule #1: HcKCR2
Supramolecule | Name: HcKCR2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Hyphochytrium catenoides (eukaryote) |
-Macromolecule #1: HcKCR2
Macromolecule | Name: HcKCR2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Hyphochytrium catenoides (eukaryote) |
Molecular weight | Theoretical: 34.023664 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MPFYDSRPPE GWPRGSVNDM DYPLLGSICA ISAIAIAGSG IWMLYRLDLG MGYSCKPYKS GRAPEVNSIS GIVCLLCGTM YAAKSFDFF DGGGTPFSLN WYWYLDYVFT CPLLIVDFAF TLDIPQKLRY SIAVFVALWC AVAAFATPSA FRFAYYALGC C WFIPLSLF ...String: MPFYDSRPPE GWPRGSVNDM DYPLLGSICA ISAIAIAGSG IWMLYRLDLG MGYSCKPYKS GRAPEVNSIS GIVCLLCGTM YAAKSFDFF DGGGTPFSLN WYWYLDYVFT CPLLIVDFAF TLDIPQKLRY SIAVFVALWC AVAAFATPSA FRFAYYALGC C WFIPLSLF LIRDVKKRYQ VYPPKCQRLL FWACVVFFGF WPLFPLLFIF SWQGSGHISR QAYYIIHAFL DLVCKSIFGF LM TFFRLEL EEHTEVQGLP LKEPKVMDAA AKSRITSEGE YIPLDQIDIN VGAPGSSLEV LFQ |
-Macromolecule #2: RETINAL
Macromolecule | Name: RETINAL / type: ligand / ID: 2 / Number of copies: 1 / Formula: RET |
---|---|
Molecular weight | Theoretical: 284.436 Da |
Chemical component information | ChemComp-RET: |
-Macromolecule #3: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)MET...
Macromolecule | Name: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE type: ligand / ID: 3 / Number of copies: 6 / Formula: PSC |
---|---|
Molecular weight | Theoretical: 759.068 Da |
Chemical component information | ChemComp-PSC: |
-Macromolecule #4: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 9 / Formula: PLM |
---|---|
Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 49 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Sugar embedding | Material: Lipid / Details: nanodisc composing of MSP1D1E3 and soybean lipid |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |