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Open data
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Basic information
Entry | Database: PDB / ID: 6zxa | ||||||||||||
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Title | LH2 complex from Marichromatium purpuratum | ||||||||||||
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Function / homology | ![]() plasma membrane light-harvesting complex / ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Gardiner, A.T. / Naydenova, K. / Castro-Hartmann, P. / Nguyen-Phan, T.C. / Russo, C.J. / Sader, K. / Hunter, C.N. / Cogdell, R.J. / Qian, P. | ||||||||||||
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. | ||||||||||||
Validation Report | ![]() ![]() ![]() | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmcif format | ![]() ![]() ![]() |
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PDB format | ![]() ![]() |
PDBML Plus | ![]() |
Others | ![]() |
-Related structure data
Related structure data | ![]() 11516CM C: citing same article ( M: map data used to model this data |
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Similar-shape strucutres |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 8015.369 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein/peptide | Mass: 5554.275 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Chemical | ChemComp-BCL / ![]() #4: Chemical | ChemComp-QS2 / #5: Chemical | ChemComp-QSE / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Light harvesting complex 2 (LH2) / Type: COMPLEX 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. Entity ID: #1-#2 / Source: NATURAL |
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Molecular weight | Value: 0.11 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 8 Details: The final buffer contains 0.02 % n-dodecyl-beta-D-maltopyranoside (DDM) |
Buffer component | Conc.: 20 mM/L / Name: Tris.HCl |
Specimen | Conc.: 5.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() Details: The sample was mono disperse with detergent beta-DDM. |
Specimen support | Details: Fischione 1070 / Grid material: ![]() |
Vitrification![]() | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blowing time, 10.0 sec. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80 K |
Image recording | Average exposure time: 0.29 sec. / Electron dose: 43.7 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9543 |
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Processing
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1330154 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 414511 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 22.55 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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