[English] 日本語
![](img/lk-miru.gif)
- EMDB-37749: In situ PBS-PSII supercomplex from cyanobacterial Spirulina platensis -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | In situ PBS-PSII supercomplex from cyanobacterial Spirulina platensis | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | complex / PHOTOSYNTHESIS | |||||||||
Function / homology | ![]() phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | You X / Zhang X / Xiao YN / Sun S / Sui SF | |||||||||
Funding support | 1 items
| |||||||||
![]() | ![]() Title: Structure of in situ PBS-PSII supercomplex at 3.5 Angstroms resolution. Authors: You X / Zhang X / Xiao YN / Sun S / Sui SF | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 228.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 52.4 KB 52.4 KB | Display Display | ![]() |
Images | ![]() | 123.6 KB | ||
Filedesc metadata | ![]() | 10.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 567.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 567.4 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wqlMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.632 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-
Sample components
+Entire : In situ PBS-PSII supercomplex
+Supramolecule #1: In situ PBS-PSII supercomplex
+Macromolecule #1: LRC1
+Macromolecule #2: LCM
+Macromolecule #3: Allophycocyanin alpha chain
+Macromolecule #4: Allophycocyanin beta chain
+Macromolecule #5: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...
+Macromolecule #6: Photosystem II protein D1
+Macromolecule #7: Photosystem II CP47 reaction center protein
+Macromolecule #8: Photosystem II CP43 reaction center protein
+Macromolecule #9: Photosystem II D2 protein
+Macromolecule #10: Cytochrome b559 subunit alpha
+Macromolecule #11: Cytochrome b559 subunit beta
+Macromolecule #12: Photosystem II reaction center protein H
+Macromolecule #13: Photosystem II reaction center protein I
+Macromolecule #14: Photosystem II reaction center protein J
+Macromolecule #15: Photosystem II reaction center protein K
+Macromolecule #16: Photosystem II reaction center protein L
+Macromolecule #17: Photosystem II reaction center protein M
+Macromolecule #18: Photosystem II extrinsic protein O
+Macromolecule #19: PsbQ protein
+Macromolecule #20: Photosystem II reaction center protein Y
+Macromolecule #21: LPP1
+Macromolecule #22: Photosystem II reaction center protein T
+Macromolecule #23: PsbU
+Macromolecule #24: Photosystem II extrinsic protein V
+Macromolecule #25: Photosystem II reaction center protein X
+Macromolecule #26: Photosystem II reaction center protein Psb30
+Macromolecule #27: Photosystem II reaction center protein Z
+Macromolecule #28: LPP2
+Macromolecule #29: Allophycocyanin beta-18 subunit
+Macromolecule #30: Allophycocyanin-B alpha subunit
+Macromolecule #31: C-phycocyanin alpha subunit
+Macromolecule #32: Phycocyanin beta subunit
+Macromolecule #33: PHYCOCYANOBILIN
+Macromolecule #34: CA-MN4-O5 CLUSTER
+Macromolecule #35: CHLORIDE ION
+Macromolecule #36: CHLOROPHYLL A
+Macromolecule #37: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #38: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #39: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #40: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #41: BICARBONATE ION
+Macromolecule #42: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #43: BETA-CAROTENE
+Macromolecule #44: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #45: PHEOPHYTIN A
+Macromolecule #46: FE (II) ION
+Macromolecule #47: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #48: CALCIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | cell |
-
Sample preparation
Buffer | pH: 7.6 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus min: 6.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |