8Z9D image
Entry Detail
PDB ID:
8Z9D
EMDB ID:
Keywords:
Title:
cryo-EM structure of PSII-LHCII megacomplex from spinach
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2024-04-23
Release Date:
2024-11-13
Method Details:
Experimental Method:
Resolution:
3.22 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Photosystem II 10 kDa polypeptide, chloroplastic
Chain IDs:V (auth: 0), X (auth: 00)
Chain Length:140
Number of Molecules:2
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Chlorophyll a-b binding protein, chloroplastic
Chain IDs:P (auth: 11), Q (auth: 22), S (auth: 1), T (auth: 2)
Chain Length:267
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Chlorophyll a-b binding protein, chloroplastic
Chain IDs:R (auth: 33), U (auth: 3)
Chain Length:264
Number of Molecules:2
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Chlorophyll a-b binding protein CP24, chloroplastic
Chain IDs:K (auth: 44), TB (auth: 4)
Chain Length:259
Number of Molecules:2
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center proteins PsbY, chloroplastic
Chain IDs:W (auth: 5), Y (auth: 55)
Chain Length:199
Number of Molecules:2
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II protein D1
Chain IDs:A, WA (auth: a), UB (auth: AA), UC (auth: Aa)
Chain Length:351
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II CP43 reaction center protein
Chain IDs:Z (auth: C), YA (auth: c), WB (auth: CC), WC (auth: Cc)
Chain Length:473
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II D2 protein
Chain IDs:AA (auth: D), ZA (auth: d), XB (auth: DD), XC (auth: Dd)
Chain Length:352
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit alpha
Chain IDs:BA (auth: E), AB (auth: e), ZB (auth: EE), YC (auth: Ee)
Chain Length:83
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit beta
Chain IDs:CA (auth: F), BB (auth: f), AC (auth: FF), ZC (auth: Ff)
Chain Length:39
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein H
Chain IDs:EA (auth: H), DB (auth: h), CC (auth: HH), BD (auth: Hh)
Chain Length:73
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein I
Chain IDs:FA (auth: I), EB (auth: i), DC (auth: II), CD (auth: Ii)
Chain Length:36
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein J
Chain IDs:GA (auth: J), FB (auth: j), EC (auth: JJ), DD (auth: Jj)
Chain Length:40
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein K
Chain IDs:HA (auth: K), GB (auth: k), FC (auth: KK), ED (auth: Kk)
Chain Length:59
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein L
Chain IDs:IA (auth: L), HB (auth: l), GC (auth: LL), FD (auth: Ll)
Chain Length:38
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein M
Chain IDs:JA (auth: M), IB (auth: m), HC (auth: MM), GD (auth: Mm)
Chain Length:34
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Oxygen-evolving enhancer protein 1, chloroplastic
Chain IDs:B (auth: Oo), LA (auth: O), KB (auth: o), JC (auth: OO)
Chain Length:332
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Oxygen-evolving enhancer protein 2, chloroplastic
Chain IDs:L (auth: Pp), N (auth: p), MA (auth: P), KC (auth: PP)
Chain Length:267
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Oxygen-evolving enhancer protein 3, chloroplastic
Chain IDs:M (auth: Qq), O (auth: q), NA (auth: Q), LC (auth: QQ)
Chain Length:232
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Chlorophyll a-b binding protein, chloroplastic
Chain IDs:C (auth: Rr), OA (auth: R), LB (auth: r), MC (auth: RR)
Chain Length:286
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Chlorophyll a-b binding protein, chloroplastic
Chain IDs:D (auth: Ss), PA (auth: S), MB (auth: s), NC (auth: SS)
Chain Length:295
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein T
Chain IDs:E (auth: Tt), QA (auth: T), NB (auth: t), OC (auth: TT)
Chain Length:33
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II 5 kDa protein, chloroplastic
Chain IDs:F (auth: Uu), RA (auth: U), OB (auth: u), PC (auth: UU)
Chain Length:99
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center W protein, chloroplastic
Chain IDs:G (auth: Ww), SA (auth: W), PB (auth: w), QC (auth: WW)
Chain Length:137
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center X protein, chloroplastic
Chain IDs:H (auth: Xx), TA (auth: X), QB (auth: x), RC (auth: XX)
Chain Length:117
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Chlorophyll a-b binding protein, chloroplastic
Chain IDs:I (auth: Yy), DA (auth: G), KA (auth: N), UA (auth: Y), CB (auth: g), JB (auth: n), RB (auth: y), BC (auth: GG), IC (auth: NN), SC (auth: YY), AD (auth: Gg), HD (auth: Nn)
Chain Length:267
Number of Molecules:12
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein Z
Chain IDs:J (auth: Zz), VA (auth: Z), SB (auth: z), TC (auth: ZZ)
Chain Length:62
Number of Molecules:4
Biological Source:Spinacia oleracea
Polymer Type:polypeptide(L)
Description:Photosystem II CP47 reaction center protein
Chain IDs:XA (auth: b), VB (auth: BB), YB (auth: B), VC (auth: Bb)
Chain Length:508
Number of Molecules:4
Biological Source:Spinacia oleracea
Primary Citation
Architecture and functional regulation of a plant PSII-LHCII megacomplex.
Sci Adv 10 eadq9967 eadq9967 (2024)
PMID: 39671473 DOI: 10.1126/sciadv.adq9967

Abstact

Photosystem II (PSII) splits water in oxygenic photosynthesis on Earth. The structure and function of the C4S4M2-type PSII-LHCII (light-harvesting complex II) megacomplexes from the wild-type and PsbR-deletion mutant plants are studied through electron microscopy (EM), structural mass spectrometry, and ultrafast fluorescence spectroscopy [time-resolved fluorescence (TRF)]. The cryo-EM structure of a type I C4S4M2 megacomplex demonstrates that the three domains of PsbR bind to the stromal side of D1, D2, and CP43; associate with the single transmembrane helix of the redox active Cyt b559; and stabilize the luminal extrinsic PsbP, respectively. This megacomplex, with PsbR and PsbY centered around the narrow interface between two dimeric PSII cores, provides the supramolecular structural basis that regulates the plastoquinone occupancy in QB site, excitation energy transfer, and oxygen evolution. PSII-LHCII megacomplexes (types I and II) and LHC aggregation levels in Arabidopsis psbR mutant were also interrogated and compared to wild-type plants through EM and picosecond TRF.

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