6L4U

Structure of the PSI-FCPI supercomplex from diatom

• PDB DOI: https://doi.org/10.2210/pdb6L4U/pdb
• EM Map EMD-0835: EMDB EMDataResource

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


• Deposited: 2019-10-21 Released: 2020-05-20 
• Deposition Author(s): Nagao, R., Kato, K., Miyazaki, N., Akita, F., Shen, J.R.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of photosystem I-light-harvesting supercomplex from a red-lineage diatom

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

(2020) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-020-16324-3

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 28-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 28-mer - A16B2C2D1E1F1G1H1I1J1K1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 997.68 kDa 
• Atom Count: 62,199 
• Modelled Residue Count: 5,205 
• Deposited Residue Count: 6,198 
• Unique protein chains: 28

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A	751	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A2	B	733	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	C	81	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit II	D	139	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV	E	67	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit III	F	185	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VIII	G [auth I]	36	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	H [auth J]	41	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XI	I [auth L]	151	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XII	J [auth M]	30	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown protein 1	K [auth 1u]	130	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit Psa28	L [auth 2u]	121	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr15	M [auth 1]	227	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr8	N [auth 2]	205	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr2	O [auth 3]	200	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr9	P [auth 4]	215	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr11	Q [auth 5]	266	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr12	R [auth 6]	208	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr10	S [auth 7]	296	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr4	T [auth 8]	270	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcf6	U [auth 9]	214	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcr3	V [auth 10]	207	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq13	W [auth 11]	229	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq3	X [auth 12]	204	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq11	Y [auth 13]	244	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq10	Z [auth 14]	249	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq8	AA [auth 15]	281	Chaetoceros neogracilis	Mutation(s): 0

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c-binding protein Lhcq5	BA [auth 16]	218	Chaetoceros neogracilis	Mutation(s): 0

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLA	AB [auth A], AD [auth B], AG [auth 2], AH [auth 4], AI [auth 5], AK [auth 8], AL [auth 9], AQ [auth 16], BB [auth A], BD [auth B], BH [auth 4], BK [auth 8], BL [auth 9], BN [auth 12], CB [auth A], CD [auth B], CH [auth 4], CK [auth 8], CL [auth 9], CN [auth 12], CP [auth 15], CQ [auth 16], DA [auth A], DB [auth A], DD [auth B], DF [auth 1], DH [auth 4], DK [auth 8], DL [auth 9], DN [auth 12], DP [auth 15], DQ [auth 16], EA [auth A], EB [auth A], ED [auth B], EF [auth 1], EH [auth 4], EP [auth 15], EQ [auth 16], FA [auth A], FB [auth A], FD [auth B], FE [auth B], FF [auth 1], FN [auth 12], FP [auth 15], FQ [auth 16], GA [auth A], GB [auth A], GD [auth B], GF [auth 1], GJ [auth 7], GK [auth 8], GP [auth 15], GQ [auth 16], HA [auth A], HB [auth A], HC [auth B], HD [auth B], HF [auth 1], HH [auth 4], HJ [auth 7], HK [auth 8], HM [auth 11], HN [auth 12], HO [auth 14], HP [auth 15], HQ [auth 16], IA [auth A], IB [auth A], IC [auth B], ID [auth B], IG [auth 3], IJ [auth 7], IO [auth 14], IP [auth 15], JA [auth A], JB [auth A], JC [auth B], JD [auth B], JE [auth F], JF [auth 1], JG [auth 3], JH [auth 4], JJ [auth 7], JM [auth 11], JO [auth 14], JP [auth 15], KA [auth A], KB [auth A], KC [auth B], KD [auth B], KE [auth F], KG [auth 3], KJ [auth 7], KO [auth 14], KP [auth 15], LA [auth A], LB [auth A], LC [auth B], LD [auth B], LE [auth F], LI [auth 6], LM [auth 11], LP [auth 15], MA [auth A], MB [auth A], MC [auth B], MD [auth B], MG [auth 3], MI [auth 6], MJ [auth 7], MM [auth 11], MO [auth 14], MP [auth 15], NA [auth A], NB [auth A], NC [auth B], ND [auth B], NG [auth 3], NI [auth 6], NJ [auth 7], NM [auth 11], NP [auth 15], OA [auth A], OB [auth A], OC [auth B], OD [auth B], OF [auth 2], OG [auth 3], OI [auth 6], OJ [auth 7], OO [auth 14], OP [auth 15], PA [auth A], PB [auth A], PC [auth B], PD [auth B], PE [auth J], PJ [auth 7], PL [auth 10], PO [auth 14], QA [auth A], QB [auth A], QC [auth B], QD [auth B], QF [auth 2], QG [auth 3], QI [auth 6], QL [auth 10], QN [auth 12], RA [auth A], RB [auth A], RC [auth B], RD [auth B], RF [auth 2], RG [auth 3], RH [auth 5], RI [auth 6], RL [auth 10], RN [auth 13], RO [auth 14], SA [auth A], SB [auth A], SC [auth B], SD [auth B], SF [auth 2], SH [auth 5], SN [auth 13], SO [auth 14], TA [auth A], TB [auth A], TC [auth B], TD [auth B], TE [auth L], TH [auth 5], TL [auth 10], TN [auth 13], UA [auth A], UC [auth B], UE [auth L], UF [auth 2], UL [auth 10], UN [auth 13], VA [auth A], VC [auth B], VF [auth 2], VI [auth 6], VK [auth 9], VL [auth 10], WA [auth A], WC [auth B], WF [auth 2], WH [auth 5], WI [auth 6], WK [auth 9], XA [auth A], XC [auth B], XF [auth 2], XH [auth 5], XI [auth 6], XK [auth 9], XL [auth 10], XM [auth 12], XN [auth 13], YA [auth A], YC [auth B], YF [auth 2], YH [auth 5], YI [auth 6], YM [auth 12], YP [auth 16], ZA [auth A], ZC [auth B], ZE [auth 2u], ZG [auth 4], ZJ [auth 8], ZK [auth 9], ZM [auth 12], ZN [auth 13], ZP [auth 16]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0	CA [auth A]	CHLOROPHYLL A ISOMER C55 H72 Mg N4 O5 VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG	AP [auth 14], BE [auth B], BF [auth 2u], DE [auth B], FC [auth A], HI [auth 5], II [auth 6], NE [auth F], RK [auth 8], SK [auth 8], TK [auth 8], XJ [auth 7], YG [auth 3]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	BC [auth A], CC [auth A], CE [auth B], DJ [auth 6], GI [auth 5], HG [auth 2], ML [auth 9]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
A86	AF [auth 2u], BJ [auth 6], BM [auth 10], CF [auth 2u], CM [auth 10], DM [auth 10], DO [auth 13], EI [auth 5], EM [auth 11], FG [auth 2], FI [auth 5], FO [auth 13], GG [auth 2], GO [auth 14], HL [auth 9], JL [auth 9], JN [auth 12], JQ [auth 16], KH [auth 4], KL [auth 9], LF [auth 1], LN [auth 12], LQ [auth 16], MH [auth 4], NH [auth 4], NK [auth 8], NL [auth 10], OL [auth 10], PF [auth 2], PH [auth 4], PP [auth 15], QH [auth 5], QK [auth 8], QP [auth 15], RM [auth 11], RP [auth 15], SJ [auth 7], SM [auth 11], TJ [auth 7], TM [auth 11], TO [auth 14], UO [auth 14], UP [auth 15], VG [auth 3], VO [auth 14], VP [auth 15], WG [auth 3], WJ [auth 7], WO [auth 14], WP [auth 15], XO [auth 14], XP [auth 15], YO [auth 14], ZO [auth 14]	(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
KC1	AN [auth 12], AO [auth 13], BG [auth 2], BI [auth 5], BO [auth 13], BQ [auth 16], CO [auth 13], EK [auth 8], EL [auth 9], EN [auth 12], FH [auth 4], FK [auth 8], FL [auth 9], GH [auth 4], GL [auth 9], GN [auth 12], IF [auth 1], IH [auth 4], IK [auth 8], IM [auth 11], IN [auth 12], IQ [auth 16], JK [auth 8], KF [auth 1], KK [auth 8], KM [auth 11], LG [auth 3], LJ [auth 7], LK [auth 8], LO [auth 14], MK [auth 8], NO [auth 14], OM [auth 11], PG [auth 3], PI [auth 6], PM [auth 11], QJ [auth 7], QO [auth 14], SG [auth 3], SI [auth 6], SL [auth 10], TF [auth 2], TI [auth 6], UH [auth 5], UI [auth 6], VH [auth 5], VN [auth 13], WL [auth 10], WN [auth 13], YK [auth 9], YL [auth 10], YN [auth 13], ZF [auth 2], ZH [auth 5]	Chlorophyll c1 C35 H30 Mg N4 O5 DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6	AJ [auth 6], AM [auth 10], CG [auth 2], CI [auth 5], CJ [auth 6], DG [auth 2], DI [auth 5], EG [auth 2], EO [auth 13], FJ [auth 7], IL [auth 9], KI [auth 6], KN [auth 12], KQ [auth 16], LH [auth 4], MF [auth 1], MN [auth 12], OH [auth 4], OK [auth 8], PK [auth 8], QM [auth 11], RJ [auth 7], SP [auth 15], TG [auth 3], TP [auth 15], UG [auth 3], UJ [auth 7], VJ [auth 7], XG [auth 3], ZI [auth 6], ZL [auth 10]	(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	AC [auth A], AE [auth B], ME [auth F], OE [auth I], QE [auth J], RE [auth J], SE [auth L], VD [auth B], VE [auth L], WB [auth A], WD [auth B], WE [auth L], XB [auth A], XD [auth B], XE [auth M], YB [auth A], YD [auth B], YE [auth 2u], ZB [auth A], ZD [auth B]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	BP [auth 15], DC [auth A], EC [auth A], EE [auth B], EJ [auth 7], FM [auth 11], GC [auth A], GE [auth B], GM [auth 11], JI [auth 6], LL [auth 9], MQ [auth 16], NF [auth 1], NN [auth 12], ON [auth 12], PN [auth 12], UK [auth 8], UM [auth 11], VM [auth 11], WM [auth 12], YJ [auth 7]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN	UB [auth A], UD [auth B]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4	HE [auth C], IE [auth C], VB [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3
MODEL REFINEMENT	PHENIX	1.13_2998

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Nagao, R., Kato, K., Miyazaki, N., Akita, F., Shen, J.R.

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release