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Yorodumi- EMDB-32228: Structure of the Acidobacteria homodimeric reaction center bound ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32228 | |||||||||
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Title | Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the larger form) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information thylakoid / iron-sulfur cluster binding / photosynthesis / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Chloracidobacterium thermophilum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.61 Å | |||||||||
Authors | Huang GQ / Dong SS / Qin XC / Sui SF | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c. Authors: Shishang Dong / Guoqiang Huang / Changhui Wang / Jiajia Wang / Sen-Fang Sui / Xiaochun Qin / Abstract: Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer ...Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer (ET) reactions. Here, we present cryo-electron microscopy (cryo-EM) structures of two forms of the RC from the microaerophilic Chloracidobacterium thermophilum (CabRC): one containing 10 subunits, including two different cytochromes; and the other possessing two additional subunits, PscB and PscZ. The larger form contained 2 Zn-bacteriochlorophylls, 16 bacteriochlorophylls, 10 chlorophylls, 2 lycopenes, 2 hemes, 3 FeS clusters, 12 lipids, 2 Ca ions and 6 water molecules, revealing a type I RC with an ET chain involving two hemes and a hybrid antenna containing bacteriochlorophylls and chlorophylls. Our results provide a structural basis for understanding the excitation energy and ET within the CabRC and offer evolutionary insights into the origin and adaptation of photosynthetic RCs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32228.map.gz | 38.4 MB | EMDB map data format | |
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Header (meta data) | emd-32228-v30.xml emd-32228.xml | 20.6 KB 20.6 KB | Display Display | EMDB header |
Images | emd_32228.png | 78.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32228 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32228 | HTTPS FTP |
-Validation report
Summary document | emd_32228_validation.pdf.gz | 463.3 KB | Display | EMDB validaton report |
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Full document | emd_32228_full_validation.pdf.gz | 462.8 KB | Display | |
Data in XML | emd_32228_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_32228_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32228 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32228 | HTTPS FTP |
-Related structure data
Related structure data | 7vzgMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32228.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : CabRC complex, the larger form
+Supramolecule #1: CabRC complex, the larger form
+Macromolecule #1: PscA
+Macromolecule #2: Cytochrome c, mono-and diheme variants
+Macromolecule #3: PscE
+Macromolecule #4: PscF
+Macromolecule #5: PscG
+Macromolecule #6: undefined polypeptide
+Macromolecule #7: Cytochrome c domain-containing protein
+Macromolecule #8: Photosystem P840 reaction center iron-sulfur protein
+Macromolecule #9: PscD'
+Macromolecule #10: [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-o...
+Macromolecule #11: BACTERIOCHLOROPHYLL A
+Macromolecule #12: CHLOROPHYLL A
+Macromolecule #13: LYCOPENE
+Macromolecule #14: CALCIUM ION
+Macromolecule #15: [(2~{R})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-m...
+Macromolecule #16: UNKNOWN LIGAND
+Macromolecule #17: [(2~{S})-2-[[(1~{R})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]met...
+Macromolecule #18: HEME C
+Macromolecule #19: [(2S)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetra...
+Macromolecule #20: IRON/SULFUR CLUSTER
+Macromolecule #21: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52612 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |