6JLU

Structure of PSII-FCP supercomplex from a centric diatom Chaetoceros gracilis at 3.02 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6JLU/pdb
• EM Map EMD-9839: EMDB EMDataResource

• Classification: PLANT PROTEIN
• Organism(s): Chaetoceros neogracilis
• Mutation(s): No 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2019-03-06 Released: 2019-07-31 
• Deposition Author(s): Pi, X., Zhao, S., Wang, W., Kuang, T., Sui, S., Shen, J.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.02 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The pigment-protein network of a diatom photosystem II-light-harvesting antenna supercomplex.

Pi, X., Zhao, S., Wang, W., Liu, D., Xu, C., Han, G., Kuang, T., Sui, S.F., Shen, J.R.

(2019) Science 365

• PubMed: 31371578 
• DOI: https://doi.org/10.1126/science.aax4406
• Primary Citation of Related Structures:  
  6JLU


• PubMed Abstract: 
  

  Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light intensity. We report a cryo-electron microscopy structure of the photosystem II (PSII)-fucoxanthin (Fx) chlorophyll (Chl) a/c binding protein (FCPII) supercomplex from the centric diatom Chaetoceros gracilis The supercomplex comprises two protomers, each with two tetrameric and three monomeric FCPIIs around a PSII core that contains five extrinsic oxygen-evolving proteins at the lumenal surface. The structure reveals the arrangement of a huge pigment network that contributes to efficient light energy harvesting, transfer, and dissipation processes in the diatoms.

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Organizational Affiliation: 

State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 70-mer - A16B4C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V2W2X2Y2Z2a2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 70-mer - A22B6C6D4E3F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 1,534.41 kDa 
• Atom Count: 102,777 
• Modelled Residue Count: 9,988 
• Deposited Residue Count: 10,296 
• Unique protein chains: 28

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbA	A, Z [auth a]	359	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbB	AA [auth b], B	509	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbC	BA [auth c], C	450	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbD	CA [auth d], D	341	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbE	DA [auth e], E	79	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbF	EA [auth f], F	32	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Psb31	FA [auth g], G	179	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	GA [auth h], H	65	Chaetoceros neogracilis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B7XBY7 (Chaetoceros neogracilis) Explore B7XBY7  Go to UniProtKB:  B7XBY7

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbI	HA [auth i], I	34	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbJ	IA [auth j], J	34	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbK	JA [auth k], K	37	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbL	KA [auth l], L	38	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbM	LA [auth m], M	41	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Psb34	MA [auth n], N	30	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Extrinsic protein in photosystem II	NA [auth o], O	249	Chaetoceros neogracilis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B6ZHE8 (Chaetoceros neogracilis) Explore B6ZHE8  Go to UniProtKB:  B6ZHE8

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
FCP-D	OA [auth p], P	226	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Extrinsic protein in photosystem II	PA [auth q], Q	211	Chaetoceros neogracilis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B6ZHE9 (Chaetoceros neogracilis) Explore B6ZHE9  Go to UniProtKB:  B6ZHE9

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbG	QA [auth r], R	73	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbT	RA [auth t], S [auth T]	31	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Extrinsic protein in photosystem II	SA [auth u], T [auth U]	93	Chaetoceros neogracilis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B6ZHF0 (Chaetoceros neogracilis) Explore B6ZHF0  Go to UniProtKB:  B6ZHF0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-550	TA [auth v], U [auth V]	137	Chaetoceros neogracilis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B6ZHF4 (Chaetoceros neogracilis) Explore B6ZHF4  Go to UniProtKB:  B6ZHF4

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbW	UA [auth w], V [auth W]	51	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center X protein	VA [auth x], W [auth X]	35	Chaetoceros neogracilis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B6ZHF2 (Chaetoceros neogracilis) Explore B6ZHF2  Go to UniProtKB:  B6ZHF2

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbY	WA [auth y], X [auth Y]	33	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbZ	XA [auth z], Y [auth Z]	61	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
FCP-E	IB [auth 10], YA [auth 0]	178	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
FCP-A	AB [auth 2], BB [auth 3], CB [auth 4], DB [auth 5], EB [auth 6], FB [auth 7], GB [auth 8], JB [auth 11], KB [auth 12], LB [auth 13], MB [auth 14], NB [auth 15], OB [auth 16], PB [auth 17], QB [auth 18], ZA [auth 1]	172	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
FCP-F	HB [auth 9], RB [auth 19]	166	Chaetoceros neogracilis	Mutation(s): 0

Small Molecules

Ligands 17 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	EI [auth h], GJ [auth w], HR [auth 11], JE [auth H], JF [auth W], NH [auth c], OH [auth c], PH [auth c], SD [auth C], TD [auth C], UD [auth C], UG [auth b], UK [auth 1], YC [auth B]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AE [auth D], AG [auth b], AH [auth c], AK [auth 0], AN [auth 5], AT [auth 14], AW [auth 19], BE [auth D], BG [auth b], BH [auth c], BJ [auth r], BM [auth 3], BO [auth 6], BP [auth 8], BR [auth 11], BT [auth 14], BV [auth 17], CD [auth C], CG [auth b], CH [auth c], CM [auth 3], CN [auth 5], CP [auth 8], CQ [auth 10], CR [auth 11], CW [auth 19], DD [auth C], DG [auth b], DH [auth c], DL [auth 2], DQ [auth 10], DT [auth 14], DW [auth 19], EC [auth B], ED [auth C], EG [auth b], EH [auth c], EL [auth 2], EN [auth 5], EP [auth 8], EQ [auth 10], ER [auth 11], ET [auth 14], EU [auth 16], EW [auth 19], FC [auth B], FD [auth C], FF [auth R], FG [auth b], FH [auth c], FJ [auth w], FN [auth 5], FR [auth 11], FU [auth 16], FW [auth 19], GC [auth B], GD [auth C], GG [auth b], GH [auth c], GL [auth 2], GQ [auth 10], GS [auth 13], HC [auth B], HD [auth C], HG [auth b], HH [auth c], HN [auth 5], HQ [auth 10], HS [auth 13], HU [auth 16], HW [auth 19], IC [auth B], ID [auth C], IF [auth W], IG [auth b], IH [auth c], IJ [auth z], IL [auth 2], IO [auth 7], IQ [auth 10], IV [auth 18], JC [auth B], JD [auth C], JG [auth b], JH [auth c], JK [auth 1], JL [auth 2], JM [auth 4], JO [auth 7], JQ [auth 10], JS [auth 13], JU [auth 16], JV [auth 18], KC [auth B], KD [auth C], KG [auth b], KJ [auth z], KK [auth 1], KU [auth 16], LC [auth B], LD [auth C], LF [auth Z], LG [auth b], LL [auth 2], LM [auth 4], LO [auth 7], LQ [auth 10], LS [auth 13], LV [auth 18], MC [auth B], MD [auth C], MG [auth b], MI [auth p], MK [auth 1], ML [auth 2], MQ [auth 10], MS [auth 13], MT [auth 15], MU [auth 16], NC [auth B], ND [auth C], NG [auth b], NI [auth p], NM [auth 4], NO [auth 7], NP [auth 9], NT [auth 15], NV [auth 18], OC [auth B], OD [auth C], OG [auth b], OI [auth p], OK [auth 1], OM [auth 4], OO [auth 7], OP [auth 9], OS [auth 13], OV [auth 18], PC [auth B], PG [auth b], PI [auth p], PK [auth 1], PS [auth 13], PT [auth 15], QC [auth B], QE [auth P], QF [auth a], QI [auth p], QM [auth 4], QO [auth 7], QP [auth 9], QR [auth 12], QV [auth 18], RC [auth B], RE [auth P], RF [auth a], RI [auth p], RJ [auth 0], RK [auth 1], RM [auth 4], RP [auth 9], RR [auth 12], RT [auth 15], SC [auth B], SE [auth P], SH [auth d], SI [auth p], SJ [auth 0], SK [auth 1], SP [auth 9], ST [auth 15], TC [auth B], TE [auth P], TF [auth a], TI [auth p], TJ [auth 0], TL [auth 3], TN [auth 6], TP [auth 9], TR [auth 12], TT [auth 15], TU [auth 17], UB [auth A], UE [auth P], UL [auth 3], UN [auth 6], UU [auth 17], VB [auth A], VE [auth P], VH [auth d], VI [auth p], VJ [auth 0], VP [auth 9], VR [auth 12], VS [auth 14], WE [auth P], WH [auth d], WJ [auth 0], WL [auth 3], WN [auth 6], WO [auth 8], WQ [auth 11], WR [auth 12], WS [auth 14], WU [auth 17], XB [auth A], XD [auth D], XE [auth P], XG [auth c], XJ [auth 0], XK [auth 1], XO [auth 8], XQ [auth 11], YG [auth c], YJ [auth 0], YL [auth 3], YN [auth 6], YR [auth 12], YS [auth 14], YU [auth 17], ZE [auth P], ZG [auth c], ZL [auth 3], ZM [auth 5], ZN [auth 6], ZO [auth 8], ZQ [auth 11], ZR [auth 12], ZU [auth 17], ZV [auth 19]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	SF [auth a], TH [auth d], WB [auth A], YD [auth D]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	AD [auth B], CC [auth A], CK [auth 0], FI [auth i], II [auth l], NE [auth L], PQ [auth 10], VF [auth a], ZB [auth A], ZF [auth b]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	BK [auth 0], CI [auth f], DF [auth P], DJ [auth w], DK [auth 1], EE [auth D], FT [auth 14], GI [auth j], GR [auth 11], HE [auth F], HF [auth W], HI [auth k], IN [auth 5], JN [auth 5], KE [auth J], KI [auth m], LE [auth K], LI [auth n], MF [auth Z], OE [auth M], OQ [auth 10], PE [auth N], QH [auth c], QQ [auth 11], RH [auth c], SM [auth 4], TG [auth b], TK [auth 1], UH [auth d], UT [auth 15], VT [auth 15], WD [auth C], XC [auth B], ZD [auth D], ZH [auth d], ZI [auth p]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	AC [auth A], CE [auth D], WF [auth a], XH [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	AJ [auth p], BC [auth A], DE [auth D], EF [auth P], EJ [auth w], FP [auth 8], GP [auth 8], GT [auth 14], JI [auth l], JJ [auth z], KN [auth 5], ME [auth L], NF [auth Z], RV [auth 18], SV [auth 18], TM [auth 4], VD [auth C], VG [auth b], WT [auth 15], XF [auth a], YH [auth d], ZC [auth B]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
A86	AF [auth P], AL [auth 2], AQ [auth 10], AS [auth 13], AU [auth 16], BL [auth 2], BQ [auth 10], BS [auth 13], BU [auth 16], CF [auth P], CL [auth 2], CO [auth 7], CS [auth 13], CU [auth 16], CV [auth 17], DM [auth 4], DO [auth 7], DS [auth 13], DU [auth 16], DV [auth 18], EK [auth 1], EM [auth 4], EO [auth 7], ES [auth 13], EV [auth 18], FK [auth 1], FM [auth 4], FO [auth 7], FS [auth 13], FV [auth 18], GK [auth 1], GM [auth 4], GO [auth 7], GV [auth 18], HK [auth 1], HM [auth 4], HO [auth 7], HP [auth 9], HT [auth 15], HV [auth 18], IK [auth 1], IM [auth 4], IP [auth 9], IR [auth 11], IT [auth 15], JP [auth 9], JR [auth 11], JT [auth 15], KP [auth 9], KR [auth 12], KT [auth 15], LJ [auth 0], LN [auth 5], LP [auth 9], LR [auth 12], LT [auth 15], MJ [auth 0], MN [auth 6], MP [auth 9], MR [auth 12], NJ [auth 0], NL [auth 3], NN [auth 6], NQ [auth 10], NR [auth 12], NU [auth 17], OJ [auth 0], OL [auth 3], ON [auth 6], OR [auth 12], OU [auth 17], PJ [auth 0], PL [auth 3], PN [auth 6], PR [auth 12], PU [auth 17], QJ [auth 0], QL [auth 3], QN [auth 6], QS [auth 14], QU [auth 17], RL [auth 3], RN [auth 6], RO [auth 8], RQ [auth 11], RS [auth 14], RU [auth 17], SL [auth 3], SN [auth 6], SO [auth 8], SQ [auth 11], SS [auth 14], SU [auth 17], TO [auth 8], TQ [auth 11], TS [auth 14], TV [auth 19], UM [auth 5], UO [auth 8], UQ [auth 11], US [auth 14], UV [auth 19], VK [auth 1], VM [auth 5], VO [auth 8], VQ [auth 11], VV [auth 19], WI [auth p], WK [auth 1], WM [auth 5], WP [auth 10], WV [auth 19], XM [auth 5], XP [auth 10], XV [auth 19], YI [auth p], YK [auth 2], YM [auth 5], YP [auth 10], YT [auth 16], YV [auth 19], ZK [auth 2], ZP [auth 10], ZT [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	AI [auth e], CJ [auth v], FE [auth E], GF [auth V]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
KC1	AM [auth 3], AO [auth 6], AV [auth 17], CT [auth 14], DP [auth 8], DR [auth 11], GN [auth 5], GW [auth 19], KL [auth 2], KQ [auth 10], LU [auth 16], NS [auth 13], PM [auth 4], PO [auth 7], PV [auth 18], QK [auth 1], UI [auth p], UP [auth 9], XR [auth 12], XT [auth 16], YE [auth P], ZJ [auth 0]	Chlorophyll c1 C35 H30 Mg N4 O5 DGNIJJSSARBJSH-QIEHNWLWSA-L
KC2	AP [auth 8], AR [auth 11], BN [auth 5], BW [auth 19], DN [auth 5], FL [auth 2], FQ [auth 10], GU [auth 16], HL [auth 2], IS [auth 13], IU [auth 16], KM [auth 4], KO [auth 7], KS [auth 13], KV [auth 18], LK [auth 1], MM [auth 4], MO [auth 7], MV [auth 18], NK [auth 1], OT [auth 15], PP [auth 9], QT [auth 15], SR [auth 12], UJ [auth 0], UR [auth 12], VL [auth 3], VN [auth 6], VU [auth 17], XL [auth 3], XN [auth 6], XS [auth 14], XU [auth 17], YO [auth 8], YQ [auth 11], ZS [auth 14]	Chlorophyll c2 C35 H28 Mg N4 O5 QDRBYWCRXZZVLY-QIEHNWLWSA-L
DD6	BF [auth P], XI [auth p]	(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol C40 H54 O3 OGHZCSINIMWCSB-WMTIXGNLSA-N
BCR	BI [auth f], DI [auth h], GE [auth F], HJ [auth y], IE [auth H], KF [auth Y], KH [auth c], LH [auth c], MH [auth c], PD [auth C], QD [auth C], QG [auth b], RD [auth C], RG [auth b], SG [auth b], UC [auth B], UF [auth a], VC [auth B], WC [auth B], YB [auth A]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
OEX	OF [auth a], SB [auth A]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT	DC [auth A], YF [auth a]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	PF [auth a], TB [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	BD [auth C], WG [auth c]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.02 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Pi, X., Zhao, S., Wang, W., Kuang, T., Sui, S., Shen, J.

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection, Database references
• Version 1.2: 2019-11-06
  Changes: Data collection, Other