4YUU image
Entry Detail
PDB ID:
4YUU
Keywords:
Title:
Crystal structure of oxygen-evolving photosystem II from a red alga
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2015-03-19
Release Date:
2016-01-20
Method Details:
Experimental Method:
Resolution:
2.77 Å
R-Value Free:
0.27
R-Value Work:
0.24
R-Value Observed:
0.25
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Photosystem II protein D1
Chain IDs:A (auth: A1), U (auth: a1), PA (auth: A2), LB (auth: a2)
Chain Length:344
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II CP47 reaction center protein
Chain IDs:B (auth: B1), V (auth: b1), QA (auth: B2), MB (auth: b2)
Chain Length:509
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II CP43 reaction center protein
Chain IDs:C (auth: C1), W (auth: c1), RA (auth: C2), NB (auth: c2)
Chain Length:460
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II D2 protein
Chain IDs:D (auth: D1), X (auth: d1), SA (auth: D2), OB (auth: d2)
Chain Length:351
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit alpha
Chain IDs:E (auth: E1), Y (auth: e1), TA (auth: E2), PB (auth: e2)
Chain Length:84
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit beta
Chain IDs:F (auth: F1), Z (auth: f1), UA (auth: F2), QB (auth: f2)
Chain Length:43
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein H
Chain IDs:G (auth: H1), AA (auth: h1), VA (auth: H2), RB (auth: h2)
Chain Length:67
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein I
Chain IDs:H (auth: I1), BA (auth: i1), WA (auth: I2), SB (auth: i2)
Chain Length:38
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein J
Chain IDs:I (auth: J1), CA (auth: j1), XA (auth: J2), TB (auth: j2)
Chain Length:39
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein K
Chain IDs:J (auth: K1), DA (auth: k1), YA (auth: K2), UB (auth: k2)
Chain Length:41
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein L
Chain IDs:K (auth: L1), EA (auth: l1), ZA (auth: L2), VB (auth: l2)
Chain Length:38
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:PHOTOSYSTEM II REACTION CENTER PROTEIN M
Chain IDs:L (auth: M1), FA (auth: m1), AB (auth: M2), WB (auth: m2)
Chain Length:108
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
Chain IDs:M (auth: O1), GA (auth: o1), BB (auth: O2), XB (auth: o2)
Chain Length:329
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:PEPTIDE CHAIN UNASSIGNED
Chain IDs:S (auth: S1), MA (auth: s1), HB (auth: S2), DC (auth: s2)
Chain Length:46
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein T
Chain IDs:N (auth: T1), HA (auth: t1), CB (auth: T2), YB (auth: t2)
Chain Length:32
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II 12 kDa extrinsic protein, chloroplastic
Chain IDs:O (auth: U1), IA (auth: u1), DB (auth: U2), ZB (auth: u2)
Chain Length:155
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Cytochrome c-550
Chain IDs:P (auth: V1), JA (auth: v1), EB (auth: V2), AC (auth: v2)
Chain Length:155
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:PEPTIDE CHAIN UNASSIGNED
Chain IDs:T (auth: W1), NA (auth: w1), IB (auth: W2), EC (auth: w2)
Chain Length:25
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:PHOTOSYSTEM II REACTION CENTER PROTEIN X
Chain IDs:R (auth: X1), LA (auth: x1), GB (auth: X2), CC (auth: x2)
Chain Length:40
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein Ycf12
Chain IDs:Q (auth: Y1), KA (auth: y1), FB (auth: Y2), BC (auth: y2)
Chain Length:35
Number of Molecules:4
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein Z
Chain IDs:KB (auth: Z2), FC (auth: z2)
Chain Length:62
Number of Molecules:2
Biological Source:Cyanidium caldarium
Polymer Type:polypeptide(L)
Description:Extrinsic protein in photosystem II
Chain IDs:OA (auth: q1), JB (auth: Q2)
Chain Length:218
Number of Molecules:2
Biological Source:Cyanidium caldarium
Primary Citation
Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga
J.Biol.Chem. 291 5676 5687 (2016)
PMID: 26757821 DOI: 10.1074/jbc.M115.711689

Abstact

Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution, which revealed the structure and interaction sites of PsbQ', a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ' subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ' were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII.

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