[English] 日本語
Yorodumi- EMDB-23563: Quantitative assessment of chlorophyll types in cryo-EM maps of p... -
+
Open data
-
Basic information
| Entry | Database: EMDB / ID: EMD-23563 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Title | Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I adapted to far-red light | |||||||||
Map data | Trimeric photosystem I adapted to far-red light from Fischerella thermalis sp. PCC 7521 | |||||||||
Sample |
| |||||||||
Keywords | Photosystem I / Photosynthesis / Far-red light / Chlorophyll f | |||||||||
| Function / homology | Function and homology information: / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / membrane => GO:0016020 / photosynthesis / endomembrane system ...: / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / membrane => GO:0016020 / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding / membrane Similarity search - Function | |||||||||
| Biological species | Fischerella thermalis PCC 7521 (bacteria) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | Gisriel CJ / Wang J | |||||||||
| Funding support | United States, 1 items
| |||||||||
Citation | Journal: BBA Adv / Year: 2021Title: Quantitative assessment of chlorophyll types in cryo-EM maps of photosystem I acclimated to far-red light Authors: Gisriel CJ / Huang HL / Reiss KM / Flesher DA / Batista VS / Bryant DA / Brudvig GW / Wang J | |||||||||
| History |
|
-
Structure visualization
| Movie |
Movie viewer |
|---|---|
| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
-
Downloads & links
-EMDB archive
| Map data | emd_23563.map.gz | 59.2 MB | EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) | emd-23563-v30.xml emd-23563.xml | 24.3 KB 24.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_23563_fsc.xml | 9.1 KB | Display | FSC data file |
| Images | emd_23563.png | 23.2 KB | ||
| Filedesc metadata | emd-23563.cif.gz | 7.6 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23563 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23563 | HTTPS FTP |
-Validation report
| Summary document | emd_23563_validation.pdf.gz | 609.7 KB | Display | EMDB validaton report |
|---|---|---|---|---|
| Full document | emd_23563_full_validation.pdf.gz | 609.3 KB | Display | |
| Data in XML | emd_23563_validation.xml.gz | 10.8 KB | Display | |
| Data in CIF | emd_23563_validation.cif.gz | 14.3 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23563 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23563 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7lx0MC M: atomic model generated by this map C: citing same article ( |
|---|---|
| Similar structure data |
-
Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
|---|---|
| Related items in Molecule of the Month |
-
Map
| File | Download / File: emd_23563.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Trimeric photosystem I adapted to far-red light from Fischerella thermalis sp. PCC 7521 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.49063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
CCP4 map header:
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Supplemental data
-
Sample components
+Entire : Photosystem I adapted to far-red light
+Supramolecule #1: Photosystem I adapted to far-red light
+Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #3: Photosystem I iron-sulfur center
+Macromolecule #4: Photosystem I protein PsaD
+Macromolecule #5: Photosystem I reaction center subunit IV
+Macromolecule #6: Photosystem I reaction center protein PsaF subunit III
+Macromolecule #7: photosystem I subunit VIII
+Macromolecule #8: Photosystem I reaction centre subunit IX / PsaJ
+Macromolecule #9: Photosystem I reaction center subunit PsaK
+Macromolecule #10: PSI subunit V
+Macromolecule #11: Photosystem I reaction center subunit XII
+Macromolecule #12: Photosystem one PsaX
+Macromolecule #13: CHLOROPHYLL A ISOMER
+Macromolecule #14: CHLOROPHYLL A
+Macromolecule #15: Chlorophyll F
+Macromolecule #16: PHYLLOQUINONE
+Macromolecule #17: IRON/SULFUR CLUSTER
+Macromolecule #18: BETA-CAROTENE
+Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #20: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #21: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #22: CALCIUM ION
-Experimental details
-Structure determination
| Method | cryo EM |
|---|---|
Processing | single particle reconstruction |
| Aggregation state | particle |
-
Sample preparation
| Concentration | 1.5 mg/mL |
|---|---|
| Buffer | pH: 7 |
| Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 |
| Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
| Microscope | FEI TITAN KRIOS |
|---|---|
| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.328 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
Movie
Controller
About Yorodumi


Keywords
Fischerella thermalis PCC 7521 (bacteria)
Authors
United States, 1 items
Citation
UCSF Chimera
















Z (Sec.)
Y (Row.)
X (Col.)






























Processing

