6J3Z

Structure of C2S1M1-type PSII-FCPII supercomplex from diatom

• PDB DOI: https://doi.org/10.2210/pdb6J3Z/pdb
• EM Map EMD-9776: EMDB EMDataResource

• Classification: ELECTRON TRANSPORT
• Organism(s): Chaetoceros neogracilis
• Mutation(s): No 


• Deposited: 2019-01-07 Released: 2019-08-07 
• Deposition Author(s): Nagao, R., Kato, K., Shen, J.R., Miyazaki, N., Akita, F.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex.

Nagao, R., Kato, K., Suzuki, T., Ifuku, K., Uchiyama, I., Kashino, Y., Dohmae, N., Akimoto, S., Shen, J.R., Miyazaki, N., Akita, F.

(2019) Nat Plants 5: 890-901

• PubMed: 31358960 
• DOI: https://doi.org/10.1038/s41477-019-0477-x
• Primary Citation of Related Structures:  
  6J3Y, 6J3Z, 6J40


• PubMed Abstract: 
  

  Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. Diatoms are one of the important groups of oxyphototrophs and possess fucoxanthin chlorophyll a/c-binding proteins (FCPs) as light harvesters. The organization and association pattern of FCP with the photosystem II (PSII) core are unknown. Here we solved the structure of PSII-FCPII supercomplexes isolated from a diatom, Chaetoceros gracilis, by single-particle cryoelectron microscopy. The PSII-FCPII forms a homodimer. In each monomer, two FCP homotetramers and three FCP monomers are associated with one PSII core. The structure reveals a highly complicated protein-pigment network that is different from the green-type light-harvesting apparatus. Comparing these two systems allows the identification of energy transfer and quenching pathways. These findings provide structural insights into not only excitation-energy transfer mechanisms in the diatom PSII-FCPII, but also changes of light harvesters between the red- and green-lineage oxyphototrophs during evolution.

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Organizational Affiliation: 

Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 59-mer - A8B4C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V2W2X2Y2Z1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 59-mer - A11B7C5D5E4F3G2H2I2J2K2L2M2N2O2P2Q2R1S1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - B4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - E2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - G2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - H2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - I2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - J2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - K2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - L2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - P2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - Q2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - R2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - S2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - T2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - U2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - V2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - W2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - X2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 14-mer - B2C2D2F2M2N2O2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 1,156.91 kDa 
• Atom Count: 74,619 
• Modelled Residue Count: 7,639 
• Deposited Residue Count: 8,367 
• Unique protein chains: 28

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein D1	A, Y [auth a]	344	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II chlorophyll protein CP47	B, Z [auth b]	509	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II chlorophyll protein CP43	AA [auth c], C	471	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein D2	BA [auth d], D	351	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	CA [auth e], E	84	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	DA [auth f], F	43	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	EA [auth h], G [auth H]	67	Chaetoceros neogracilis	Mutation(s): 0
UniProt
Find proteins for B7XBY7 (Chaetoceros gracilis) Explore B7XBY7  Go to UniProtKB:  B7XBY7

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	FA [auth i], H [auth I]	38	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	GA [auth j], I [auth J]	39	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	HA [auth k], J [auth K]	44	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	IA [auth l], K [auth L]	38	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	JA [auth m], L [auth M]	131	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Extrinsic protein in photosystem II	KA [auth o], M [auth O]	248	Chaetoceros neogracilis	Mutation(s): 0
UniProt
Find proteins for B6ZHE8 (Chaetoceros gracilis) Explore B6ZHE8  Go to UniProtKB:  B6ZHE8

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	LA [auth t], N [auth T]	31	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Extrinsic protein in photosystem II	MA [auth u], O [auth U]	93	Chaetoceros neogracilis	Mutation(s): 0
UniProt
Find proteins for B6ZHF0 (Chaetoceros gracilis) Explore B6ZHF0  Go to UniProtKB:  B6ZHF0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-550	NA [auth v], P [auth V]	137	Chaetoceros neogracilis	Mutation(s): 0
UniProt
Find proteins for B6ZHF4 (Chaetoceros gracilis) Explore B6ZHF4  Go to UniProtKB:  B6ZHF4

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Ycf12	OA [auth y], Q [auth Y]	34	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center X protein	PA [auth x], R [auth X]	38	Chaetoceros neogracilis	Mutation(s): 0
UniProt
Find proteins for B6ZHF2 (Chaetoceros gracilis) Explore B6ZHF2  Go to UniProtKB:  B6ZHF2

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	QA [auth z], S [auth Z]	61	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Extrinsic protein in photosystem II	RA [auth q], T [auth Q]	155	Chaetoceros neogracilis	Mutation(s): 0
UniProt
Find proteins for B6ZHE9 (Chaetoceros gracilis) Explore B6ZHE9  Go to UniProtKB:  B6ZHE9

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein W	SA [auth w], U [auth W]	72	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown protein 0	TA [auth 5], V [auth 0]	31	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown protein 1	UA [auth 6], W [auth 1]	30	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown protein 2	VA [auth 7], X [auth 2]	10	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1	AB [auth 15], BB [auth 16], CB [auth 17], DB [auth 18], WA [auth 11], XA [auth 12], YA [auth 13], ZA [auth 14]	207	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein monomer 1	EB [auth 19]	215	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein monomer 2	FB [auth 20]	143	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein monomer 3	GB [auth 21]	155	Chaetoceros neogracilis	Mutation(s): 0

Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	ED [auth C], FD [auth C], FG [auth c], GG [auth c], UD [auth H], VD [auth J], XG [auth h], YG [auth j]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AC [auth B], AD [auth C], AF [auth b], AG [auth c], AJ [auth 13], AK [auth 15], AL [auth 17], AM [auth 18], BC [auth B], BD [auth C], BF [auth b], BG [auth c], BH [auth m], BI [auth 12], BJ [auth 13], BK [auth 15], BM [auth 18], CC [auth B], CD [auth C], CF [auth b], CG [auth c], CK [auth 15], CL [auth 17], DC [auth B], DF [auth b], DI [auth 12], DK [auth 15], DL [auth 17], EC [auth B], EE [auth Z], EF [auth b], EI [auth 12], EK [auth 15], EL [auth 17], EN [auth 21], FF [auth b], FH [auth z], FI [auth 12], FK [auth 15], FL [auth 17], FM [auth 19], FN [auth 21], GF [auth b], GI [auth 12], GL [auth 17], GM [auth 19], GN [auth 21], HD [auth C], HE [auth W], HH [auth w], HI [auth 12], HL [auth 17], HM [auth 19], HN [auth 21], IB [auth A], ID [auth C], IE [auth W], IH [auth w], II [auth 12], IJ [auth 14], IL [auth 17], IM [auth 19], IN [auth 21], JD [auth D], JH [auth 11], JI [auth 12], JJ [auth 14], JL [auth 17], JM [auth 19], JN [auth 21], KB [auth A], KD [auth D], KG [auth d], KH [auth 11], KI [auth 12], KJ [auth 14], KM [auth 19], KN [auth 21], LE [auth a], LG [auth d], LH [auth 11], LI [auth 12], LJ [auth 14], LM [auth 19], LN [auth 21], MC [auth B], ME [auth a], MH [auth 11], MI [auth 12], MJ [auth 14], MM [auth 19], MN [auth 21], ND [auth D], NF [auth b], NH [auth 11], NJ [auth 14], NK [auth 16], NM [auth 19], OD [auth D], OH [auth 11], OJ [auth 14], OK [auth 16], PG [auth d], PH [auth 11], PJ [auth 14], PK [auth 16], QB [auth B], QC [auth C], QF [auth c], QG [auth d], QH [auth 11], QJ [auth 14], QK [auth 16], QL [auth 18], RB [auth B], RC [auth C], RF [auth c], RH [auth 11], RJ [auth 14], RK [auth 16], SB [auth B], SC [auth C], SE [auth b], SF [auth c], SK [auth 16], SL [auth 18], SM [auth 20], TB [auth B], TC [auth C], TE [auth b], TF [auth c], TI [auth 13], TK [auth 16], TL [auth 18], TM [auth 20], UB [auth B], UC [auth C], UE [auth b], UF [auth c], UI [auth 13], UK [auth 16], UL [auth 18], UM [auth 20], VB [auth B], VC [auth C], VE [auth b], VF [auth c], VI [auth 13], VK [auth 16], VL [auth 18], VM [auth 20], WB [auth B], WC [auth C], WE [auth b], WF [auth c], WI [auth 13], WL [auth 18], WM [auth 20], XB [auth B], XC [auth C], XE [auth b], XF [auth c], XH [auth 11], XI [auth 13], XJ [auth 15], XL [auth 18], XM [auth 20], YB [auth B], YC [auth C], YE [auth b], YF [auth c], YI [auth 13], YJ [auth 15], YL [auth 18], YM [auth 20], ZB [auth B], ZC [auth C], ZD [auth M], ZE [auth b], ZF [auth c], ZI [auth 13], ZJ [auth 15], ZL [auth 18], ZM [auth 20]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	JB [auth A], LD [auth D], MG [auth d], NG [auth d]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	KC [auth B], LF [auth b], MB [auth A], OE [auth a], YD [auth L], ZG [auth l]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	AE [auth M], CH [auth m], FE [auth Q], GE [auth W], GH [auth w], HG [auth c], IC [auth B], JC [auth B], JE [auth 1], JF [auth b], KF [auth b], QD [auth D], TG [auth d], ZH [auth 12]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	MD [auth D], OG [auth d], PD [auth D], RG [auth d]	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE C53 H80 O2 FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG	AH [auth l], LC [auth B], MF [auth b], OB [auth A], QE [auth a], SG [auth d], WD [auth L], XD [auth L]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
A86	AN [auth 20], BL [auth 17], BN [auth 20], CI [auth 12], CJ [auth 13], CM [auth 18], CN [auth 20], DJ [auth 13], DM [auth 18], DN [auth 20], EJ [auth 13], EM [auth 18], FJ [auth 13], GJ [auth 13], GK [auth 15], HJ [auth 14], HK [auth 15], IK [auth 15], JK [auth 15], KK [auth 15], KL [auth 17], LK [auth 15], LL [auth 17], MK [auth 15], ML [auth 17], NI [auth 12], NL [auth 17], NN [auth 21], OI [auth 12], OL [auth 17], OM [auth 19], ON [auth 21], PI [auth 12], PL [auth 17], PM [auth 19], PN [auth 21], QI [auth 12], QM [auth 19], QN [auth 21], RI [auth 12], RL [auth 18], RM [auth 20], RN [auth 21], SH [auth 11], SI [auth 13], SJ [auth 14], TH [auth 11], TJ [auth 14], UH [auth 11], UJ [auth 14], VH [auth 11], VJ [auth 14], WH [auth 11], WJ [auth 14], WK [auth 16], XK [auth 16], YH [auth 11], YK [auth 16], ZK [auth 16]	(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate C42 H58 O6 SJWWTRQNNRNTPU-XJUZQKKNSA-N
HEM	BE [auth V], EH [auth v], SD [auth F], VG [auth f]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BCR	CE [auth Y], DD [auth C], DE [auth Z], DG [auth c], DH [auth m], EG [auth c], FC [auth B], GC [auth B], GD [auth C], HC [auth B], HF [auth b], IF [auth b], IG [auth c], JG [auth c], LB [auth A], NC [auth B], NE [auth a], OF [auth b], PB [auth A], RD [auth F], RE [auth a], TD [auth H], UG [auth f], WG [auth h]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMU	AI [auth 12], OC [auth B]	DODECYL-ALPHA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-YHBSTRCHSA-N
OEX	PC [auth C], PF [auth c]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT	NB [auth A], PE [auth a]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	HB [auth A], KE [auth a]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX	1.13_2998

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Nagao, R., Kato, K., Shen, J.R., Miyazaki, N., Akita, F.

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection, Database references
• Version 1.2: 2019-08-28
  Changes: Data collection, Database references
• Version 1.3: 2019-11-06
  Changes: Data collection, Other