6J40

Structure of C2S2M2-type PSII-FCPII supercomplex from diatom

• PDB DOI: https://doi.org/10.2210/pdb6J40/pdb
• EM Map EMD-9777: EMDB EMDataResource

• Classification: ELECTRON TRANSPORT
• Organism(s): Chaetoceros neogracilis
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• 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: 3.80 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 70-mer - A16B4C4D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V2W2X2Y2Z2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 70-mer - A21B7C5D5E4F3G2H2I2J2K2L2M2N2O2P2Q2R1S1T1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 1,510.99 kDa 
• Atom Count: 96,390 
• Modelled Residue Count: 9,560 
• Deposited Residue Count: 10,536 
• 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  Membrane Entity: Yes
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  Membrane Entity: Yes
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  Membrane Entity: Yes
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  Membrane Entity: Yes
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  Membrane Entity: Yes
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  Membrane Entity: Yes
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], HB [auth 31], IB [auth 32], JB [auth 33], KB [auth 34], LB [auth 35], MB [auth 36], NB [auth 37], OB [auth 38], 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], PB [auth 39]	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], QB [auth 40]	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], RB [auth 41]	155	Chaetoceros neogracilis	Mutation(s): 0

Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	FE [auth H], GE [auth J], KH [auth h], LH [auth j], OD [auth C], PD [auth C], PG [auth c], QG [auth c]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AD [auth C], AG [auth c], AI [auth 11], AK [auth 14], AL [auth 16], AP [auth 32], AR [auth 35], AS [auth 37], AT [auth 39], AU [auth 41], BC [auth B], BD [auth C], BG [auth c], BI [auth 11], BK [auth 14], BL [auth 16], BP [auth 32], BS [auth 37], BT [auth 39], BU [auth 41], CC [auth B], CD [auth C], CF [auth b], CG [auth c], CH [auth d], CI [auth 11], CK [auth 14], CL [auth 16], CP [auth 32], CS [auth 37], CT [auth 39], CU [auth 41], DC [auth B], DD [auth C], DF [auth b], DG [auth c], DH [auth d], DI [auth 11], DK [auth 14], DL [auth 16], DM [auth 18], DP [auth 32], DS [auth 37], DT [auth 39], DU [auth 41], EC [auth B], ED [auth C], EF [auth b], EG [auth c], EI [auth 11], EK [auth 14], EL [auth 16], EN [auth 20], EO [auth 31], EP [auth 32], EQ [auth 34], ES [auth 37], ET [auth 39], EU [auth 41], FC [auth B], FD [auth C], FF [auth b], FG [auth c], FK [auth 14], FL [auth 16], FM [auth 18], FN [auth 20], FO [auth 31], FP [auth 32], FQ [auth 34], FT [auth 39], FU [auth 41], GC [auth B], GD [auth C], GF [auth b], GG [auth c], GJ [auth 13], GL [auth 16], GM [auth 18], GN [auth 20], GO [auth 31], GP [auth 32], GQ [auth 34], GT [auth 39], GU [auth 41], HC [auth B], HD [auth C], HF [auth b], HG [auth c], HJ [auth 13], HL [auth 16], HM [auth 18], HN [auth 20], HO [auth 31], HQ [auth 34], HT [auth 39], IC [auth B], ID [auth C], IF [auth b], IG [auth c], IJ [auth 13], IL [auth 16], IM [auth 18], IN [auth 20], IO [auth 31], IQ [auth 34], IR [auth 36], JC [auth B], JD [auth C], JF [auth b], JG [auth c], JJ [auth 13], JM [auth 18], JN [auth 20], JO [auth 31], JQ [auth 34], JR [auth 36], KC [auth B], KD [auth C], KE [auth M], KF [auth b], KG [auth c], KI [auth 11], KJ [auth 13], KK [auth 15], KM [auth 18], KN [auth 20], KO [auth 31], KQ [auth 34], KR [auth 36], LC [auth B], LD [auth C], LF [auth b], LG [auth c], LJ [auth 13], LK [auth 15], LM [auth 18], LN [auth 20], LO [auth 31], LQ [auth 34], LR [auth 36], LS [auth 38], MC [auth B], MD [auth C], MF [auth b], MG [auth c], MJ [auth 13], MK [auth 15], MM [auth 18], MO [auth 31], MQ [auth 34], MR [auth 36], MT [auth 40], NC [auth B], NF [auth b], NJ [auth 13], NK [auth 15], NL [auth 17], NM [auth 18], NP [auth 33], NQ [auth 34], NR [auth 36], NS [auth 38], NT [auth 40], OC [auth B], OF [auth b], OH [auth m], OI [auth 12], OJ [auth 13], OK [auth 15], OM [auth 18], OR [auth 36], OS [auth 38], OT [auth 40], PC [auth B], PE [auth Z], PF [auth b], PK [auth 15], PL [auth 17], PP [auth 33], PR [auth 36], PS [auth 38], PT [auth 40], QF [auth b], QI [auth 12], QK [auth 15], QL [auth 17], QN [auth 21], QP [auth 33], QR [auth 36], QS [auth 38], QT [auth 40], RD [auth C], RI [auth 12], RK [auth 15], RL [auth 17], RN [auth 21], RP [auth 33], RS [auth 38], RT [auth 40], SD [auth C], SE [auth W], SH [auth z], SI [auth 12], SK [auth 15], SL [auth 17], SM [auth 19], SN [auth 21], SO [auth 31], SP [auth 33], SQ [auth 35], SS [auth 38], ST [auth 40], TB [auth A], TD [auth C], TE [auth W], TI [auth 12], TL [auth 17], TM [auth 19], TN [auth 21], TP [auth 33], TQ [auth 35], TS [auth 38], TT [auth 40], UD [auth D], UG [auth c], UH [auth w], UI [auth 12], UL [auth 17], UM [auth 19], UN [auth 21], UP [auth 33], UQ [auth 35], US [auth 38], VB [auth A], VD [auth D], VE [auth a], VG [auth c], VH [auth w], VI [auth 12], VL [auth 17], VM [auth 19], VN [auth 21], VP [auth 33], VQ [auth 35], VR [auth 37], VS [auth 38], WE [auth a], WG [auth c], WH [auth 11], WI [auth 12], WJ [auth 14], WL [auth 17], WM [auth 19], WN [auth 21], WO [auth 32], WP [auth 33], WQ [auth 35], WS [auth 38], XC [auth B], XF [auth b], XG [auth d], XH [auth 11], XI [auth 12], XJ [auth 14], XM [auth 19], XN [auth 21], XP [auth 33], XQ [auth 35], XR [auth 37], YD [auth D], YG [auth d], YH [auth 11], YI [auth 12], YJ [auth 14], YM [auth 19], YN [auth 21], YO [auth 32], YQ [auth 35], YR [auth 37], YT [auth 41], ZD [auth D], ZH [auth 11], ZI [auth 12], ZJ [auth 14], ZM [auth 19], ZO [auth 32], ZQ [auth 35], ZR [auth 37], ZT [auth 41]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	AH [auth d], UB [auth A], WD [auth D], ZG [auth d]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	JE [auth L], MH [auth l], VC [auth B], VF [auth b], XB [auth A], YE [auth a]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	BE [auth D], GH [auth d], LE [auth M], MI [auth 12], PH [auth m], QE [auth Q], RE [auth W], RG [auth c], TC [auth B], TF [auth b], TH [auth w], UC [auth B], UF [auth b], UO [auth 32]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	AE [auth D], BH [auth d], EH [auth d], XD [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	AF [auth a], FH [auth d], HE [auth L], IE [auth L], NH [auth l], WC [auth B], WF [auth b], ZB [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
A86	AJ [auth 12], AM [auth 17], AN [auth 19], AO [auth 21], AQ [auth 33], BJ [auth 12], BM [auth 17], BN [auth 19], BO [auth 21], BQ [auth 33], BR [auth 35], CJ [auth 12], CM [auth 17], CN [auth 19], CO [auth 21], CQ [auth 33], CR [auth 35], DJ [auth 12], DN [auth 20], DO [auth 21], DQ [auth 33], DR [auth 35], EJ [auth 12], EM [auth 18], ER [auth 35], FI [auth 11], FJ [auth 13], FR [auth 35], FS [auth 37], GI [auth 11], GK [auth 14], GR [auth 35], GS [auth 37], HI [auth 11], HK [auth 14], HP [auth 32], HR [auth 35], HS [auth 37], HU [auth 41], II [auth 11], IK [auth 14], IP [auth 32], IS [auth 37], IT [auth 39], IU [auth 41], JI [auth 11], JK [auth 14], JL [auth 16], JP [auth 32], JS [auth 37], JT [auth 39], JU [auth 41], KL [auth 16], KP [auth 32], KS [auth 37], KT [auth 39], KU [auth 41], LI [auth 11], LL [auth 16], LP [auth 32], LT [auth 40], LU [auth 41], ML [auth 16], MN [auth 20], MP [auth 32], MS [auth 38], NN [auth 20], NO [auth 31], OL [auth 17], ON [auth 20], OO [auth 31], OP [auth 33], OQ [auth 34], PI [auth 12], PJ [auth 13], PM [auth 18], PN [auth 20], PO [auth 31], PQ [auth 34], QJ [auth 13], QM [auth 18], QO [auth 31], QQ [auth 34], RJ [auth 13], RM [auth 18], RO [auth 31], RQ [auth 34], RR [auth 36], SJ [auth 13], SR [auth 36], TJ [auth 13], TK [auth 15], TO [auth 31], TR [auth 36], UJ [auth 13], UK [auth 15], UR [auth 36], UT [auth 40], VJ [auth 13], VK [auth 15], VT [auth 40], WK [auth 15], WR [auth 37], WT [auth 40], XK [auth 15], XL [auth 17], XO [auth 32], XS [auth 38], XT [auth 40], YK [auth 15], YL [auth 17], YP [auth 33], YS [auth 38], ZK [auth 15], ZL [auth 17], ZN [auth 21], ZP [auth 33], ZS [auth 38]	(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	CE [auth E], HH [auth e], ME [auth V], RH [auth v]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BCR	AC [auth A], BF [auth a], DE [auth F], EE [auth H], IH [auth f], JH [auth h], ND [auth C], NE [auth Y], NG [auth c], OE [auth Z], OG [auth c], QC [auth B], QD [auth C], QH [auth m], RC [auth B], RF [auth b], SC [auth B], SF [auth b], SG [auth c], TG [auth c], WB [auth A], XE [auth a], YC [auth B], YF [auth b]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMU	NI [auth 12], VO [auth 32]	DODECYL-ALPHA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-YHBSTRCHSA-N
OEX	ZC [auth C], ZF [auth c]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT	YB [auth A], ZE [auth a]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	SB [auth A], UE [auth a]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 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