[English] 日本語
Yorodumi- EMDB-41460: Structure of a mutated photosystem II complex reveals perturbatio... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41460 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of a mutated photosystem II complex reveals perturbation of the oxygen-evolving complex | |||||||||
Map data | Sharpened map masked | |||||||||
Sample |
| |||||||||
Keywords | photosynthesis / photosystem II / oxygen-evolving complex / D1-D170E / S1 state / transition metals / metalloenzyme | |||||||||
Function / homology | Function and homology information plasma membrane-derived thylakoid photosystem II / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide ...plasma membrane-derived thylakoid photosystem II / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / extrinsic component of membrane / photosystem II / photosynthesis, light reaction / phosphate ion binding / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / calcium ion binding / heme binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.14 Å | |||||||||
Authors | Flesher DA / Liu J / Wang J / Gisriel CJ / Yang KR / Batista VS / Debus RJ / Brudvig GW | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: J Biol Chem / Year: 2024 Title: Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels. Authors: David A Flesher / Jinchan Liu / Jimin Wang / Christopher J Gisriel / Ke R Yang / Victor S Batista / Richard J Debus / Gary W Brudvig / Abstract: Photosystem II (PSII) is the water-plastoquinone photo-oxidoreductase central to oxygenic photosynthesis. PSII has been extensively studied for its ability to catalyze light-driven water oxidation at ...Photosystem II (PSII) is the water-plastoquinone photo-oxidoreductase central to oxygenic photosynthesis. PSII has been extensively studied for its ability to catalyze light-driven water oxidation at a MnCaO cluster called the oxygen-evolving complex (OEC). Despite these efforts, the complete reaction mechanism for water oxidation by PSII is still heavily debated. Previous mutagenesis studies have investigated the roles of conserved amino acids, but these studies have lacked a direct structural basis that would allow for a more meaningful interpretation. Here, we report a 2.14-Å resolution cryo-EM structure of a PSII complex containing the substitution Asp170Glu on the D1 subunit. This mutation directly perturbs a bridging carboxylate ligand of the OEC, which alters the spectroscopic properties of the OEC without fully abolishing water oxidation. The structure reveals that the mutation shifts the position of the OEC within the active site without markedly distorting the MnCaO cluster metal-metal geometry, instead shifting the OEC as a rigid body. This shift disturbs the hydrogen-bonding network of structured waters near the OEC, causing disorder in the conserved water channels. This mutation-induced disorder appears consistent with previous FTIR spectroscopic data. We further show using quantum mechanics/molecular mechanics methods that the mutation-induced structural changes can affect the magnetic properties of the OEC by altering the axes of the Jahn-Teller distortion of the Mn(III) ion coordinated to D1-170. These results offer new perspectives on the conserved water channels, the rigid body property of the OEC, and the role of D1-Asp170 in the enzymatic water oxidation mechanism. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_41460.map.gz | 30.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-41460-v30.xml emd-41460.xml | 51.9 KB 51.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41460_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_41460.png | 142.6 KB | ||
Filedesc metadata | emd-41460.cif.gz | 9.4 KB | ||
Others | emd_41460_additional_1.map.gz emd_41460_additional_2.map.gz emd_41460_additional_3.map.gz emd_41460_additional_4.map.gz emd_41460_additional_5.map.gz emd_41460_additional_6.map.gz emd_41460_half_map_1.map.gz emd_41460_half_map_2.map.gz | 138.5 MB 152.8 MB 92.8 MB 152.5 MB 152.5 MB 166.8 MB 139 MB 138.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41460 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41460 | HTTPS FTP |
-Validation report
Summary document | emd_41460_validation.pdf.gz | 870.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_41460_full_validation.pdf.gz | 870.2 KB | Display | |
Data in XML | emd_41460_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | emd_41460_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41460 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41460 | HTTPS FTP |
-Related structure data
Related structure data | 8towMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_41460.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map masked | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Unsharpened map
File | emd_41460_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Scaled D170E map
File | emd_41460_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Scaled D170E map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Local Resolution Map
File | emd_41460_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Local Resolution Map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: D170E-minus-WT difference map
File | emd_41460_additional_4.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | D170E-minus-WT difference map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Scaled WT map
File | emd_41460_additional_5.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Scaled WT map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Sharpened map non-masked
File | emd_41460_additional_6.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map non-masked | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1
File | emd_41460_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2
File | emd_41460_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : photosystem II
+Supramolecule #1: photosystem II
+Macromolecule #1: Photosystem II protein D1 2
+Macromolecule #2: Photosystem II CP47 reaction center protein
+Macromolecule #3: Photosystem II CP43 reaction center protein
+Macromolecule #4: Photosystem II D2 protein
+Macromolecule #5: Cytochrome b559 subunit alpha
+Macromolecule #6: Cytochrome b559 subunit beta
+Macromolecule #7: Photosystem II reaction center protein H
+Macromolecule #8: Photosystem II reaction center protein I
+Macromolecule #9: Photosystem II reaction center protein J
+Macromolecule #10: Photosystem II reaction center protein K
+Macromolecule #11: Photosystem II reaction center protein L
+Macromolecule #12: Photosystem II reaction center protein M
+Macromolecule #13: Photosystem II manganese-stabilizing polypeptide
+Macromolecule #14: Sll1638 protein
+Macromolecule #15: Photosystem II protein Y
+Macromolecule #16: Photosystem II reaction center protein T
+Macromolecule #17: Photosystem II 12 kDa extrinsic protein
+Macromolecule #18: Cytochrome c-550
+Macromolecule #19: Photosystem II reaction center X protein
+Macromolecule #20: Photosystem II reaction center protein Ycf12
+Macromolecule #21: Photosystem II reaction center protein Z
+Macromolecule #22: CA-MN4-O5 CLUSTER
+Macromolecule #23: FE (II) ION
+Macromolecule #24: CHLORIDE ION
+Macromolecule #25: CHLOROPHYLL A
+Macromolecule #26: PHEOPHYTIN A
+Macromolecule #27: BETA-CAROTENE
+Macromolecule #28: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #29: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #30: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #31: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #32: BICARBONATE ION
+Macromolecule #33: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #34: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #35: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #36: (3R)-beta,beta-caroten-3-ol
+Macromolecule #37: CALCIUM ION
+Macromolecule #38: water
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |