8Z9D image
Deposition Date 2024-04-23
Release Date 2024-11-13
Last Version Date 2025-02-26
Entry Detail
PDB ID:
8Z9D
Keywords:
PHOTOSYNTHESIS
Title:
cryo-EM structure of PSII-LHCII megacomplex from spinach
Biological Source:
Source Organism:
Spinacia oleracea (Taxon ID: 3562)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.22 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8Z9D validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II 10 kDa polypeptide, chloroplastic
Gene (Uniprot):PSBR
Chain IDs:V (auth: 0), X (auth: 00)
Chain Length:140
Number of Molecules:2
Biological Source:Spinacia oleracea
UniProt ID:P10690 Pfam ID:PF04725
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
UniProt ID:P12333
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chlorophyll a-b binding protein, chloroplastic
Gene (Uniprot):LOC110800942
Chain IDs:R (auth: 33), U (auth: 3)
Chain Length:264
Number of Molecules:2
Biological Source:Spinacia oleracea
UniProt ID:A0A9R0J656 Pfam ID:PF00504
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
UniProt ID:P36494 Pfam ID:PF00504
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center proteins PsbY, chloroplastic
Gene (Uniprot):PSBY
Chain IDs:W (auth: 5), Y (auth: 55)
Chain Length:199
Number of Molecules:2
Biological Source:Spinacia oleracea
UniProt ID:P80470 Pfam ID:PF06298 EC:1.97.1.12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1
Gene (Uniprot):psbA
Chain IDs:A, WA (auth: a), UB (auth: AA), UC (auth: Aa)
Chain Length:351
Number of Molecules:4
Biological Source:Spinacia oleracea
UniProt ID:P69560 Pfam ID:PF00124
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
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
UniProt ID:P06003 Pfam ID:PF00421
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD
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
UniProt ID:P06005 Pfam ID:PF00124
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
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
UniProt ID:P69383 Pfam ID:PF00283, PF00284
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
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
UniProt ID:P60128 Pfam ID:PF00283
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
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
UniProt ID:P05146 Pfam ID:PF00737
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
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
UniProt ID:P62103 Pfam ID:PF02532
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
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
UniProt ID:Q9M3L2 Pfam ID:PF01788
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
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
UniProt ID:P12163 Pfam ID:PF02533
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
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
UniProt ID:P60150 Pfam ID:PF02419
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
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
UniProt ID:P62112 Pfam ID:PF05151
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Oxygen-evolving enhancer protein 1, chloroplastic
Gene (Uniprot):PSBO
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
UniProt ID:P12359 Pfam ID:PF01716
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Oxygen-evolving enhancer protein 2, chloroplastic
Gene (Uniprot):PSBP
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
UniProt ID:P12302 Pfam ID:PF01789
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Oxygen-evolving enhancer protein 3, chloroplastic
Gene (Uniprot):PSBQ
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
UniProt ID:P12301 Pfam ID:PF05757
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chlorophyll a-b binding protein, chloroplastic
Gene (Uniprot):LOC110775011
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
UniProt ID:A0A9R0HRF2 Pfam ID:PF00504
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chlorophyll a-b binding protein, chloroplastic
Gene (Uniprot):LOC110790014
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
UniProt ID:A0A9R0IJF3 Pfam ID:PF00504
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
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
UniProt ID:P61840 Pfam ID:PF01405
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II 5 kDa protein, chloroplastic
Gene (Uniprot):LOC110801337
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
UniProt ID:A0A9R0J8H2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center W protein, chloroplastic
Gene (Uniprot):psbW
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
UniProt ID:Q41387 Pfam ID:PF07123
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center X protein, chloroplastic
Gene (Uniprot):LOC110783121
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
UniProt ID:A0A9R0JQ89 Pfam ID:PF06596
Protein Blast
Polymer Type:polypeptide(L)
Molecule: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
UniProt ID:P12333
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
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
UniProt ID:Q9M3M6 Pfam ID:PF01737
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
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
UniProt ID:P04160 Pfam ID:PF00421
Ligand Molecules
BCR
BCT
CHL
CL
CLA
DGD
FE2
HEM
LHG
LMG
LMU
LUT
NEX
OEX
PHO
PL9
SQD
XAT
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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Protein

Chemical

Disease

Primary Citation of related structures
8Z9D