5B5M image
Entry Detail
PDB ID:
5B5M
Keywords:
Title:
Crystal structure of the Sr-substituted LH1-RC complex from Tch. tepidum
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2016-05-12
Release Date:
2017-03-22
Method Details:
Experimental Method:
Resolution:
3.30 Å
R-Value Free:
0.30
R-Value Work:
0.27
R-Value Observed:
0.27
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:LH1 alpha polypeptide
Chain IDs:E (auth: A), G (auth: D), I (auth: F), K (auth: I), M (auth: K), O, Q, S, U, W, Y, AA (auth: 1), CA (auth: 3), EA (auth: 5), GA (auth: 7), IA (auth: 9), OA (auth: m), QA (auth: p), SA (auth: r), UA (auth: u), WA (auth: w), YA (auth: AA), AB (auth: AC), CB (auth: AE), EB (auth: AG), GB (auth: AI), IB (auth: AK), KB (auth: d), MB (auth: f), OB (auth: h), QB (auth: j), SB (auth: l)
Chain Length:61
Number of Molecules:32
Biological Source:Thermochromatium tepidum
Polymer Type:polypeptide(L)
Description:LH1 beta polypeptide
Chain IDs:F (auth: B), H (auth: E), J (auth: G), L (auth: J), N, P, R, T, V, X, Z, BA (auth: 2), DA (auth: 4), FA (auth: 6), HA (auth: 8), JA (auth: 0), PA (auth: n), RA (auth: q), TA (auth: s), VA (auth: v), XA (auth: z), ZA (auth: AB), BB (auth: AD), DB (auth: AF), FB (auth: AH), HB (auth: AJ), JB (auth: AL), LB (auth: e), NB (auth: g), PB (auth: i), RB (auth: k), TB (auth: c)
Chain Length:47
Number of Molecules:32
Biological Source:Thermochromatium tepidum
Polymer Type:polypeptide(L)
Description:Photosynthetic reaction center cytochrome c subunit
Chain IDs:A (auth: C), KA (auth: o)
Chain Length:47
Number of Molecules:2
Biological Source:Thermochromatium tepidum
Polymer Type:polypeptide(L)
Description:Photosynthetic reaction center H subunit
Chain IDs:D (auth: H), NA (auth: t)
Chain Length:61
Number of Molecules:2
Biological Source:Thermochromatium tepidum
Polymer Type:polypeptide(L)
Description:Photosynthetic reaction center L subunit
Chain IDs:B (auth: L), LA (auth: x)
Chain Length:61
Number of Molecules:2
Biological Source:Thermochromatium tepidum
Polymer Type:polypeptide(L)
Description:Photosynthetic reaction center M subunit
Chain IDs:C (auth: M), MA (auth: y)
Chain Length:61
Number of Molecules:2
Biological Source:Thermochromatium tepidum
Primary Citation
Structural Basis for the Unusual Qy Red-Shift and Enhanced Thermostability of the LH1 Complex from Thermochromatium tepidum.
Biochemistry 55 6495 6504 (2016)
PMID: 27933779 DOI: 10.1021/acs.biochem.6b00742

Abstact

While the majority of the core light-harvesting complexes (LH1) in purple photosynthetic bacteria exhibit a Qy absorption band in the range of 870-890 nm, LH1 from the thermophilic bacterium Thermochromatium tepidum displays the Qy band at 915 nm with an enhanced thermostability. These properties are regulated by Ca2+ ions. Substitution of the Ca2+ with other divalent metal ions results in a complex with the Qy band blue-shifted to 880-890 nm and a reduced thermostability. Following the recent publication of the structure of the Ca-bound LH1-reaction center (RC) complex [Niwa, S., et al. (2014) Nature 508, 228], we have determined the crystal structures of the Sr- and Ba-substituted LH1-RC complexes with the LH1 Qy band at 888 nm. Sixteen Sr2+ and Ba2+ ions are identified in the LH1 complexes. Both Sr2+ and Ba2+ are located at the same positions, and these are clearly different from, though close to, the Ca2+-binding sites. Conformational rearrangement induced by the substitution is limited to the metal-binding sites. Unlike the Ca-LH1-RC complex, only the α-polypeptides are involved in the Sr and Ba coordinations in LH1. The difference in the thermostability between these complexes can be attributed to the different patterns of the network formed by metal binding. The Sr- and Ba-LH1-RC complexes form a single-ring network by the LH1 α-polypeptides only, in contrast to the double-ring network composed of both α- and β-polypeptides in the Ca-LH1-RC complex. On the basis of the structural information, a combined effect of hydrogen bonding, structural integrity, and charge distribution is considered to influence the spectral properties of the core antenna complex.

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