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Yorodumi- EMDB-51760: Cryo-EM structure of RC-dLH complex model I from Gem. groenlandic... -
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Open data
- Basic information
Basic information
| Entry |  | |||||||||
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| Title | Cryo-EM structure of RC-dLH complex model I from Gem. groenlandica strain TET16 | |||||||||
|  Map data | ||||||||||
|  Sample | 
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|  Keywords | reaction centre light harvesting complex / RC-dLH / photosynthetic bacteria / gemmatimonas groenlandica / PHOTOSYNTHESIS | |||||||||
| Function / homology |  Function and homology information organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / endomembrane system / electron transfer activity / iron ion binding / heme binding / metal ion binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / endomembrane system / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane Similarity search - Function | |||||||||
| Biological species |  Gemmatimonas groenlandica (bacteria) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
|  Authors | Gardiner A / Qian P / Koblizek M / Jing Y / Joosten M / Jakobi A / Bina D / Mujakic I / Gardian Z / Kaftan D / Castro-Hartmann P | |||||||||
| Funding support |  Czech Republic, 1 items 
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|  Citation |  Journal: To Be Published Title: Cryo-EM structure of RC-dLH complex model I from Gem. groenlandica strain TET16 Authors: Gardiner A / Qian P / Koblizek M / Jing Y / Joosten M / Jakobi A / Bina D / Mujakic I / Gardian Z / Kaftan D / Castro-Hartmann P | |||||||||
| History | 
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- Structure visualization
Structure visualization
| Supplemental images | 
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- Downloads & links
Downloads & links
-EMDB archive
| Map data |  emd_51760.map.gz | 777.7 MB |  EMDB map data format | |
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| Header (meta data) |  emd-51760-v30.xml  emd-51760.xml | 33.8 KB 33.8 KB | Display Display |  EMDB header | 
| FSC (resolution estimation) |  emd_51760_fsc.xml | 19.8 KB | Display |  FSC data file | 
| Images |  emd_51760.png | 74.6 KB | ||
| Filedesc metadata |  emd-51760.cif.gz | 8.8 KB | ||
| Others |  emd_51760_half_map_1.map.gz  emd_51760_half_map_2.map.gz | 764 MB 764 MB | ||
| Archive directory |  http://ftp.pdbj.org/pub/emdb/structures/EMD-51760  ftp://ftp.pdbj.org/pub/emdb/structures/EMD-51760 | HTTPS FTP | 
-Validation report
| Summary document |  emd_51760_validation.pdf.gz | 1.2 MB | Display |  EMDB validaton report | 
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| Full document |  emd_51760_full_validation.pdf.gz | 1.2 MB | Display | |
| Data in XML |  emd_51760_validation.xml.gz | 29.9 KB | Display | |
| Data in CIF |  emd_51760_validation.cif.gz | 39.5 KB | Display | |
| Arichive directory |  https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51760  ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51760 | HTTPS FTP | 
-Related structure data
| Related structure data |  9h19MC M: atomic model generated by this map C: citing same article ( | 
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| Similar structure data | Similarity search - Function & homology  F&H Search | 
- Links
Links
| EMDB pages |  EMDB (EBI/PDBe) /  EMDataResource | 
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| Related items in Molecule of the Month | 
- Map
Map
| File |  Download / File: emd_51760.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
 
 Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.732 Å | ||||||||||||||||||||||||||||||||||||
| Density | 
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML: 
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-Supplemental data
-Half map: z-flip
| File | emd_51760_half_map_1.map | ||||||||||||
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| Annotation | z-flip | ||||||||||||
| Projections & Slices | 
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| Density Histograms | 
-Half map: z-flip
| File | emd_51760_half_map_2.map | ||||||||||||
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| Annotation | z-flip | ||||||||||||
| Projections & Slices | 
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| Density Histograms | 
- Sample components
Sample components
+Entire : RC-dLH complex model I from Gemmatimonas groenlandica
+Supramolecule #1: RC-dLH complex model I from Gemmatimonas groenlandica
+Macromolecule #1: Light-harvesting protein
+Macromolecule #2: Light-harvesting protein
+Macromolecule #3: reaction centre S sub unit
+Macromolecule #4: Reaction center protein L chain
+Macromolecule #5: Reaction center protein M chain
+Macromolecule #6: reaction centre Ht sub unit
+Macromolecule #7: reaction centre Hc sub unit
+Macromolecule #8: Photosynthetic reaction center cytochrome c subunit
+Macromolecule #9: Light-harvesting protein
+Macromolecule #10: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{...
+Macromolecule #11: BACTERIOCHLOROPHYLL A
+Macromolecule #12: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #13: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
+Macromolecule #14: MENAQUINONE 8
+Macromolecule #15: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...
+Macromolecule #16: BACTERIOPHEOPHYTIN A
+Macromolecule #17: FE (III) ION
+Macromolecule #18: SPIRILLOXANTHIN
+Macromolecule #19: HEME C
+Macromolecule #20: water
-Experimental details
-Structure determination
| Method | cryo EM | 
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|  Processing | single particle reconstruction | 
| Aggregation state | particle | 
- Sample preparation
Sample preparation
| Concentration | 4.0 mg/mL | 
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| Buffer | pH: 8 / Component - Concentration: 20.0 mM / Component - Name: Tris-HCL / Details: 20 mM Tris-HCL, 50 mM NaCl, pH 8.0, 0.02% beta-DDM | 
| Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | 
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 3 seconds, blot force, 3. | 
| Details | Protein in buffer solution with detergent of beta-DDM | 
- Electron microscopy
Electron microscopy
| Microscope | TFS KRIOS | 
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| Temperature | Min: 88.0 K / Max: 92.0 K | 
| Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV Details: Thermofisher Titan Krios G3 with energy filter selectrisX | 
| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 23012 / Average exposure time: 5.13 sec. / Average electron dose: 60.0 e/Å2 | 
| Electron beam | Acceleration voltage: 300 kV / Electron source:  FIELD EMISSION GUN | 
| Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000 | 
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN | 
| Experimental equipment |  Model: Titan Krios / Image courtesy: FEI Company | 
+ Image processing
Image processing
-Atomic model buiding 1
| Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model | 
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| Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 60 / Target criteria: model to map | 
| Output model |  PDB-9h19:  | 
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