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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11516 | ||||||||||||
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Title | LH2 complex from Marichromatium purpuratum | ||||||||||||
![]() | A cryo-EM map of the light harvesting complex 2 (LH2) from a photosynthetic bacterium Marichromatium purpuratum. | ||||||||||||
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![]() | photosynthesis / purple bacteria / light harvesting complex / Marichromatium purpuratum / okenone. | ||||||||||||
Function / homology | ![]() : / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane => GO:0016020 / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.38 Å | ||||||||||||
![]() | Gardiner AT / Naydenova K | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The 2.4 Å cryo-EM structure of a heptameric light-harvesting 2 complex reveals two carotenoid energy transfer pathways. Authors: Alastair T Gardiner / Katerina Naydenova / Pablo Castro-Hartmann / Tu C Nguyen-Phan / Christopher J Russo / Kasim Sader / C Neil Hunter / Richard J Cogdell / Pu Qian / ![]() ![]() Abstract: We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from () determined by cryogenic electron microscopy. The structure contains a heptameric ring that is ...We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from () determined by cryogenic electron microscopy. The structure contains a heptameric ring that is unique among all known LH2 structures, explaining the unusual spectroscopic properties of this bacterial antenna complex. We identify two sets of distinct carotenoids in the structure and describe a network of energy transfer pathways from the carotenoids to bacteriochlorophyll molecules. The geometry imposed by the heptameric ring controls the resonant coupling of the long-wavelength energy absorption band. Together, these details reveal key aspects of the assembly and oligomeric form of purple bacterial LH2 complexes that were previously inaccessible by any technique. | ||||||||||||
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 | ![]() | 32 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.3 KB 17.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 189.7 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zxaMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 12.2 TB Data #1: Unaligned multi-frame micrographs of purple bacterial LH2 on HexAuFoil supports [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | A cryo-EM map of the light harvesting complex 2 (LH2) from a photosynthetic bacterium Marichromatium purpuratum. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.646 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 : Light harvesting complex 2 (LH2)
Entire | Name: Light harvesting complex 2 (LH2) |
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Components |
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-Supramolecule #1: Light harvesting complex 2 (LH2)
Supramolecule | Name: Light harvesting complex 2 (LH2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: The LH2 complex from Mar. purpuratum forms a circular heptameter. Each subunit consists of an alpha/beta pair, in which all pigment molecules, three Bchl a and two carotenoids are bound non-covalently. |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 110 KDa |
-Macromolecule #1: LHC domain-containing protein
Macromolecule | Name: LHC domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 8.015369 KDa |
Sequence | String: MKVPVMMADE SIATINHPED DWKIWTVINP ATWMVPFFGI LFVQMWLIHS YALSLPGYGF KDSVRVAQPA UniProtKB: LHC domain-containing protein |
-Macromolecule #2: Light-harvesting protein B:800-850 subunit beta
Macromolecule | Name: Light-harvesting protein B:800-850 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 5.554275 KDa |
Sequence | String: ADPKAANLSG LTDAQAKEFH EHWKHGVWSW VMIASAVHVV TWIYQPWF UniProtKB: Light-harvesting protein B:800-850 subunit beta |
-Macromolecule #3: BACTERIOCHLOROPHYLL A
Macromolecule | Name: BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 21 / Formula: BCL |
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Molecular weight | Theoretical: 911.504 Da |
Chemical component information | ![]() ChemComp-BCL: |
-Macromolecule #4: 9-cis-okenone
Macromolecule | Name: 9-cis-okenone / type: ligand / ID: 4 / Number of copies: 7 / Formula: QS2 |
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Molecular weight | Theoretical: 578.866 Da |
Chemical component information | ![]() ChemComp-QS2: |
-Macromolecule #5: all-trans okenone
Macromolecule | Name: all-trans okenone / type: ligand / ID: 5 / Number of copies: 7 / Formula: QSE |
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Molecular weight | Theoretical: 578.866 Da |
Chemical component information | ![]() ChemComp-QSE: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5.5 mg/mL |
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Buffer | pH: 8 / Component - Concentration: 20.0 mM/L / Component - Name: Tris.HCl Details: The final buffer contains 0.02 % n-dodecyl-beta-D-maltopyranoside (DDM) |
Grid | Model: Homemade / Material: GOLD / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.0067 kPa / Details: Fischione 1070 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Blowing time, 10.0 sec.. |
Details | The sample was mono disperse with detergent beta-DDM. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9543 / Average exposure time: 0.29 sec. / Average electron dose: 43.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.4 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: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 22.55 | ||||||
Output model | ![]() PDB-6zxa: |