8ASL image
Deposition Date 2022-08-19
Release Date 2023-08-16
Last Version Date 2024-10-16
Entry Detail
PDB ID:
8ASL
Keywords:
PHOTOSYNTHESIS
Title:
RCII/PSI complex, class 2
Biological Source:
Source Organism:
Synechocystis sp. PCC 6803 (Taxon ID: 1148)
Host Organism:
Synechocystis sp. PCC 6803
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.15 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8ASL validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1 2
Gene (Uniprot):psbA2, psbA3
Chain IDs:L (auth: A)
Chain Length:751
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P16033 Pfam ID:PF00124 EC:1.10.3.9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD
Chain IDs:M (auth: D)
Chain Length:336
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P09192 Pfam ID:PF00124
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:N (auth: E)
Chain Length:74
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P09190 Pfam ID:PF00283, PF00284
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:O (auth: F)
Chain Length:44
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P09191 Pfam ID:PF00283
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:P (auth: I)
Chain Length:40
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:Q54697 Pfam ID:PF02532
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II assembly lipoprotein Ycf48
Gene (Uniprot):ycf48
Chain IDs:Q (auth: S)
Chain Length:342
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P73069
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I P700 chlorophyll a apoprotein A1
Gene (Uniprot):psaA
Chain IDs:A (auth: a)
Chain Length:751
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P29254 Pfam ID:PF00223 EC:1.97.1.12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I P700 chlorophyll a apoprotein A2
Gene (Uniprot):psaB
Chain IDs:B (auth: b)
Chain Length:731
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P29255 Pfam ID:PF00223 EC:1.97.1.12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I iron-sulfur center
Gene (Uniprot):psaC
Chain IDs:C (auth: c)
Chain Length:81
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P32422 Pfam ID:PF12838 EC:1.97.1.12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I reaction center subunit II
Gene (Uniprot):psaD
Chain IDs:D (auth: d)
Chain Length:336
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P19569 Pfam ID:PF02531
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I reaction center subunit IV
Gene (Uniprot):psaE
Chain IDs:E (auth: e)
Chain Length:74
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P12975 Pfam ID:PF02427
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I reaction center subunit III
Gene (Uniprot):psaF
Chain IDs:F (auth: f)
Chain Length:44
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P29256 Pfam ID:PF02507
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I reaction center subunit VIII
Gene (Uniprot):psaI
Chain IDs:G (auth: i)
Chain Length:40
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:Q55330 Pfam ID:PF00796
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I reaction center subunit IX
Gene (Uniprot):psaJ
Chain IDs:H (auth: j)
Chain Length:40
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:Q55329 Pfam ID:PF01701
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I reaction center subunit PsaK 1
Gene (Uniprot):psaK1
Chain IDs:I (auth: k)
Chain Length:86
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P72712 Pfam ID:PF01241
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I reaction center subunit XI
Gene (Uniprot):psaL
Chain IDs:J (auth: l)
Chain Length:157
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P37277 Pfam ID:PF02605
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem I reaction center subunit XII
Gene (Uniprot):psaM
Chain IDs:K (auth: m)
Chain Length:31
Number of Molecules:1
Biological Source:Synechocystis sp. PCC 6803
UniProt ID:P72986 Pfam ID:PF07465
Ligand Molecules
45D
BCR
CL0
CLA
ECH
EQ3
FE2
HEM
LHG
LMG
LMT
PHO
PQN
SF4
ZEX
Primary Citation
The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis.
Nat Commun 14 4681 4681 (2023)
PMID: 37542031 DOI: 10.1038/s41467-023-40388-6

Abstact

Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
8AM5