7YMI image
Deposition Date 2022-07-28
Release Date 2023-08-16
Last Version Date 2024-09-04
Entry Detail
PDB ID:
7YMI
Keywords:
PHOTOSYNTHESIS
Title:
PSII-Pcb Dimer of Acaryochloris Marina
Biological Source:
Source Organism:
Acaryochloris marina MBIC11017 (Taxon ID: 329726)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7YMI validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:High light inducible protein
Gene (Uniprot):hli
Chain IDs:R (auth: 1), LA (auth: 5)
Chain Length:356
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C576 Pfam ID:PF00421
Protein Blast
Polymer Type:polypeptide(L)
Molecule:High light inducible protein
Gene (Uniprot):hli
Chain IDs:P (auth: 2), JA (auth: 6)
Chain Length:352
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C3E5 Pfam ID:PF00421
Protein Blast
Polymer Type:polypeptide(L)
Molecule:High light inducible protein
Gene (Uniprot):hli
Chain IDs:S (auth: 3), MA (auth: 7)
Chain Length:349
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C6I0 Pfam ID:PF00421
Protein Blast
Polymer Type:polypeptide(L)
Molecule:High light inducible protein
Gene (Uniprot):hli
Chain IDs:T (auth: 4), NA (auth: 8)
Chain Length:353
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C3E6 Pfam ID:PF00421
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1 2
Gene (Uniprot):psbA2, psbA3
Chain IDs:A, U (auth: a)
Chain Length:360
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:A5A8K9 Pfam ID:PF00124
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
Chain IDs:B, V (auth: b)
Chain Length:506
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0CFM2 Pfam ID:PF00421
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
Chain IDs:C, W (auth: c)
Chain Length:490
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C1V7 Pfam ID:PF00421
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein 1
Gene (Uniprot):psbD1, psbD2
Chain IDs:D, X (auth: d)
Chain Length:351
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C1V6 Pfam ID:PF00124
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E, Y (auth: e)
Chain Length:83
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C6T2 Pfam ID:PF00283, PF00284
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein Y
Gene (Uniprot):psbF
Chain IDs:F, Z (auth: f)
Chain Length:99
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C2V2 Pfam ID:PF00283
Polymer Type:polypeptide(L)
Molecule:Unknown protein
Chain IDs:Q (auth: G), KA (auth: g)
Chain Length:41
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II 10 kDa phosphoprotein PsbH
Gene (Uniprot):psbH
Chain IDs:G (auth: H), AA (auth: h)
Chain Length:71
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0CDZ2 Pfam ID:PF00737
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein PsbI
Gene (Uniprot):psbI
Chain IDs:H (auth: I), BA (auth: i)
Chain Length:34
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C5R5 Pfam ID:PF02532
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:I (auth: K), CA (auth: k)
Chain Length:45
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C6Z7 Pfam ID:PF02533
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:J (auth: L), DA (auth: l)
Chain Length:38
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C6T1 Pfam ID:PF02419
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
Chain IDs:K (auth: M), EA (auth: m)
Chain Length:34
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0CFM0 Pfam ID:PF05151
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:L (auth: T), FA (auth: t)
Chain Length:46
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C605 Pfam ID:PF01405
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center X protein
Gene (Uniprot):psbX
Chain IDs:M (auth: X), GA (auth: x)
Chain Length:40
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0BYW9 Pfam ID:PF06596
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Ycf12
Chain IDs:N (auth: Y), HA (auth: y)
Chain Length:39
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:A0AAJ6N611
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:O (auth: Z), IA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Acaryochloris marina MBIC11017
UniProt ID:B0C0S7 Pfam ID:PF01737
Ligand Molecules
8CT
BCT
CL7
DGD
FE2
HEM
LHG
LMG
PHO
PL9
SQD
ZEX
Primary Citation
Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll d -containing cyanobacterium.
Sci Adv 10 eadk7140 eadk7140 (2024)
PMID: 38394197 DOI: 10.1126/sciadv.adk7140

Abstact

Acaryochloris marina is a unique cyanobacterium using chlorophyll d (Chl d) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of A. marina associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from A. marina at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization.

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Protein

Chemical

Disease

Primary Citation of related structures
7YMI