+Open data
-Basic information
Entry | Database: PDB / ID: 7zdi | ||||||
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Title | PucB-LH2 complex from Rps. palustris | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / light harvesting complex 2 / LH2 / Rps. palustris / purple bacteria / cryo-EM / single particle analysis | ||||||
Function / homology | Function and homology information organelle inner membrane / 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 | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Qian, P. / Cogdell, R.J. / Nguyen-Phan, T.C. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Cryo-EM structures of light-harvesting 2 complexes from reveal the molecular origin of absorption tuning. Authors: Pu Qian / Cam T Nguyen-Phan / Alastair T Gardiner / Tristan I Croll / Aleksander W Roszak / June Southall / Philip J Jackson / Cvetelin Vasilev / Pablo Castro-Hartmann / Kasim Sader / C Neil ...Authors: Pu Qian / Cam T Nguyen-Phan / Alastair T Gardiner / Tristan I Croll / Aleksander W Roszak / June Southall / Philip J Jackson / Cvetelin Vasilev / Pablo Castro-Hartmann / Kasim Sader / C Neil Hunter / Richard J Cogdell / Abstract: The genomes of some purple photosynthetic bacteria contain a multigene family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) ...The genomes of some purple photosynthetic bacteria contain a multigene family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) complexes. To unravel this complexity, we generated four sets of deletion mutants in , each encoding a single type of gene pair and enabling the purification of complexes designated as PucA-LH2, PucB-LH2, PucD-LH2, and PucE-LH2. The structures of all four purified LH2 complexes were determined by cryogenic electron microscopy (cryo-EM) at resolutions ranging from 2.7 to 3.6 Å. Uniquely, each of these complexes contains a hitherto unknown polypeptide, γ, that forms an extended undulating ribbon that lies in the plane of the membrane and that encloses six of the nine LH2 αβ-subunits. The γ-subunit, which is located near to the cytoplasmic side of the complex, breaks the C9 symmetry of the LH2 complex and binds six extra bacteriochlorophylls (BChls) that enhance the 800-nm absorption of each complex. The structures show that all four complexes have two complete rings of BChls, conferring absorption bands centered at 800 and 850 nm on the PucA-LH2, PucB-LH2, and PucE-LH2 complexes, but, unusually, the PucD-LH2 antenna has only a single strong near-infared (NIR) absorption peak at 803 nm. Comparison of the cryo-EM structures of these LH2 complexes reveals altered patterns of hydrogen bonds between LH2 αβ-side chains and the bacteriochlorin rings, further emphasizing the major role that H bonds play in spectral tuning of bacterial antenna complexes. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Qian, P. / Cogdell, R.J. #2: Journal: To Be Published Title: Cryo-EM structures of light harvesting complex 2 from Rhodopseudomonas palustris: a molecular origin of spectroscopic variation Authors: Qian, P. / Cogdell, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zdi.cif.gz | 313.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zdi.ent.gz | 224.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/7zdi ftp://data.pdbj.org/pub/pdb/validation_reports/zd/7zdi | HTTPS FTP |
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-Related structure data
Related structure data | 14650MC 7zcuC 7ze3C 7ze8C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 6873.004 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: A0A323UGK7 #2: Protein | Mass: 5738.550 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: A0A2R4GZC1 #3: Protein | | Mass: 10848.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: A0A2R4GRK2 #4: Chemical | ChemComp-BCL / #5: Chemical | ChemComp-IRM / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PucB-LH2 from Rps. palustris / Type: COMPLEX / Details: Delt-pucBA(aced) / Entity ID: #1-#3 / Source: NATURAL |
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Source (natural) | Organism: Rhodopseudomonas palustris ATCC 17001 (phototrophic) |
Buffer solution | pH: 8 / Details: 0.1% LDAO in 20 mM Tris.Cl pH 8.0 |
Buffer component | Conc.: 20 mM / Name: Tris.HCl / Formula: C4H11NO3 |
Specimen | Conc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: protein was purified using LDAO detergent. |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: Chamber humidity: 100%; Chamber temperature: 4 oC; Blotting time: 2.5; Blotting force: 3; Wait time: 30 sec |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80 K |
Image recording | Average exposure time: 12.21 sec. / Electron dose: 44.1 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5593 / Details: Images were collected in AFIS mode. |
EM imaging optics | Details: No energy filter was applied. |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1946434 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 402668 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.44 Å2 | ||||||||||||||||||||||||||||||||||||
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