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- EMDB-9107: A unique supramolecular organization of photosystem I in the moss... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9107 | |||||||||
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Title | A unique supramolecular organization of photosystem I in the moss Physcomitrella patens | |||||||||
![]() | Large Physcomitrella patens PSI-LHCI supercomplex map from cryo-EM | |||||||||
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![]() | photosynthesis / complex / photosystem I / light harvesting complex / Physcomitrella | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.6 Å | |||||||||
![]() | Iwai M / Grob P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A unique supramolecular organization of photosystem I in the moss Physcomitrella patens. Authors: Masakazu Iwai / Patricia Grob / Anthony T Iavarone / Eva Nogales / Krishna K Niyogi / ![]() Abstract: The photosynthesis machinery in chloroplast thylakoid membranes is comprised of multiple protein complexes and supercomplexes. Here, we show a novel supramolecular organization of photosystem I (PSI) ...The photosynthesis machinery in chloroplast thylakoid membranes is comprised of multiple protein complexes and supercomplexes. Here, we show a novel supramolecular organization of photosystem I (PSI) in the moss Physcomitrella patens by single-particle cryo-electron microscopy. The moss-specific light-harvesting complex (LHC) protein Lhcb9 is involved in this PSI supercomplex, which has been shown to have a molecular density similar to that of the green alga Chlamydomonas reinhardtii. Our results show that the structural organization is unexpectedly different-two rows of the LHCI belt exist as in C. reinhardtii, but the outer one is shifted toward the PsaK side. Furthermore, one trimeric LHC protein and one monomeric LHC protein position alongside PsaL/K, filling the gap between these subunits and the outer LHCI belt. We provide evidence showing that Lhcb9 is a key factor, acting as a linkage between the PSI core and the outer LHCI belt to form the unique supramolecular organization of the PSI supercomplex in P. patens. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 55.4 KB 55.4 KB | Display Display | ![]() |
Images | ![]() | 294.5 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6memMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Large Physcomitrella patens PSI-LHCI supercomplex map from cryo-EM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Large PSI-LHCI supercomplex
+Supramolecule #1: Large PSI-LHCI supercomplex
+Macromolecule #1: Chlorophyll A/B binding protein 1
+Macromolecule #2: Chlorophyll A/B binding protein 5
+Macromolecule #3: Chlorophyll A/B binding protein 3
+Macromolecule #4: Chlorophyll A/B binding protein 7
+Macromolecule #5: Chlorophyll A/B binding protein 4
+Macromolecule #6: Chlorophyll A/B binding protein 9
+Macromolecule #7: Chlorophyll A/B binding protein 8
+Macromolecule #8: Chlorophyll A/B binding protein 2
+Macromolecule #9: Chlorophyll A/B binding protein 6
+Macromolecule #10: PsaA
+Macromolecule #11: Chlorophyll A/B binding protein 10
+Macromolecule #12: PsaB
+Macromolecule #13: Chlorophyll A/B binding protein 11
+Macromolecule #14: PsaC
+Macromolecule #15: Chlorophyll A/B binding protein 12
+Macromolecule #16: PsaD
+Macromolecule #17: PsaE
+Macromolecule #18: PsaF
+Macromolecule #19: PsaG
+Macromolecule #20: PsaH
+Macromolecule #21: PsaI
+Macromolecule #22: PsaJ
+Macromolecule #23: PsaK
+Macromolecule #24: PsaL
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL | ||||||||
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Buffer | pH: 6.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: Lights off, blot 4.5 seconds before plunging.. |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 93.0 K / Max: 93.0 K |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 3 / Number real images: 361 / Average exposure time: 0.5 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: -4.2 µm / Calibrated defocus min: -1.9000000000000001 µm / Calibrated magnification: 107140 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: -1.8 µm / Nominal defocus min: -2.5 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-6mem: |