6PNJ | pdb_00006pnj

Structure of Photosystem I Acclimated to Far-red Light

• PDB DOI: https://doi.org/10.2210/pdb6PNJ/pdb
• EM Map EMD-20397: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Fischerella thermalis PCC 7521
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2019-07-02 Released: 2020-02-12 
• Deposition Author(s): Gisriel, C.J., Shen, G., Kurashov, V., Ho, M., Zhang, S., Williams, D., Golbeck, J.H., Fromme, P., Bryant, D.A.
• Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States), National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The structure of Photosystem I acclimated to far-red light illuminates an ecologically important acclimation process in photosynthesis

Gisriel, C., Shen, G., Kurashov, V., Ho, M.Y., Zhang, S., Williams, D., Golbeck, J.H., Fromme, P., Bryant, D.A.

(2020) Sci Adv 6: eaay6415

• DOI: https://doi.org/10.1126/sciadv.aay6415

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 36-mer - A3B3C3D3E3F3G3H3I3J3K3L3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 36-mer - A6B6C3D3E3F3G3H3I3J3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 1,115.87 kDa 
• Atom Count: 71,511 
• Modeled Residue Count: 6,708 
• Deposited Residue Count: 7,380 
• Unique protein chains: 12

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A, G, Y [auth a]	788	Fischerella thermalis PCC 7521	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for G6FME9 (Fischerella thermalis JSC-11) Explore G6FME9  Go to UniProtKB:  G6FME9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A2	B, H, Z [auth b]	741	Fischerella thermalis PCC 7521	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for G6FMF0 (Fischerella thermalis JSC-11) Explore G6FMF0  Go to UniProtKB:  G6FMF0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	AA [auth c], C, N	81	Fischerella thermalis PCC 7521	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for B0CB42 (Acaryochloris marina (strain MBIC 11017)) Explore B0CB42  Go to UniProtKB:  B0CB42

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I protein PsaD	BA [auth d], D, O	159	Fischerella thermalis PCC 7521	Mutation(s): 0
UniProt
Find proteins for G6FW99 (Fischerella thermalis JSC-11) Explore G6FW99  Go to UniProtKB:  G6FW99

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV	CA [auth e], E, P	72	Fischerella thermalis PCC 7521	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for G6FQU3 (Fischerella thermalis JSC-11) Explore G6FQU3  Go to UniProtKB:  G6FQU3

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center protein PsaF subunit III	DA [auth f], F, Q	159	Fischerella thermalis PCC 7521	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for G6FMD3 (Fischerella thermalis JSC-11) Explore G6FMD3  Go to UniProtKB:  G6FMD3

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
photosystem I subunit VIII	EA [auth i], I, R	67	Fischerella thermalis PCC 7521	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A1U7GTG5 (Fischerella major NIES-592) Explore A0A1U7GTG5  Go to UniProtKB:  A0A1U7GTG5

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction centre subunit IX / PsaJ	FA [auth j], J, S	48	Fischerella thermalis PCC 7521	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for G6FMD2 (Fischerella thermalis JSC-11) Explore G6FMD2  Go to UniProtKB:  G6FMD2

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
photosystem I reaction center subunit PsaK	GA [auth k], K, T	39	Fischerella thermalis PCC 7521	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for G6FV28 (Fischerella thermalis JSC-11) Explore G6FV28  Go to UniProtKB:  G6FV28

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center protein subunit XI	HA [auth l], L, U	174	Fischerella thermalis PCC 7521	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for G6FMF1 (Fischerella thermalis JSC-11) Explore G6FMF1  Go to UniProtKB:  G6FMF1

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XII	IA [auth m], M, V	31	Fischerella thermalis PCC 7521	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for G6FWT6 (Fischerella thermalis JSC-11) Explore G6FWT6  Go to UniProtKB:  G6FWT6

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem one PsaX	JA [auth x], W, X	101	Fischerella thermalis PCC 7521	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for G6FSH2 (Fischerella thermalis JSC-11) Explore G6FSH2  Go to UniProtKB:  G6FSH2

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F6C	GB [auth A], GI [auth H], GN [auth b], HB [auth A], NF [auth G], NN [auth b], OF [auth G], SD [auth B], UK [auth a], VK [auth a], ZD [auth B], ZH [auth H]	Chlorophyll F C55 H68 Mg N4 O6 YUTLCKLMRUVWDE-FOFJUSMOSA-M
CLA	AB [auth A], AD [auth B], AE [auth B], AF [auth G], AG [auth G], AH [auth H], AI [auth H], AK [auth a], AL [auth a], AM [auth b], AN [auth b], BB [auth A], BD [auth B], BE [auth B], BF [auth G], BG [auth G], BH [auth H], BI [auth H], BJ [auth L], BK [auth a], BL [auth a], BM [auth b], BN [auth b], CB [auth A], CD [auth B], CF [auth G], CG [auth G], CH [auth H], CI [auth H], CJ [auth L], CK [auth a], CL [auth a], CM [auth b], CN [auth b], DB [auth A], DD [auth B], DF [auth G], DG [auth G], DH [auth H], DI [auth H], DJ [auth L], DK [auth a], DL [auth a], DM [auth b], DN [auth b], EB [auth A], ED [auth B], EF [auth G], EG [auth G], EH [auth H], EI [auth H], EK [auth a], EL [auth a], EM [auth b], EN [auth b], FB [auth A], FD [auth B], FF [auth G], FG [auth G], FH [auth H], FI [auth H], FK [auth a], FL [auth a], FM [auth b], FN [auth b], GD [auth B], GF [auth G], GG [auth G], GH [auth H], GK [auth a], GL [auth a], GM [auth b], HD [auth B], HF [auth G], HH [auth H], HI [auth H], HK [auth a], HL [auth a], HM [auth b], HN [auth b], IB [auth A], ID [auth B], IF [auth G], IH [auth H], II [auth H], IK [auth a], IL [auth a], IM [auth b], IN [auth b], IO [auth k], JB [auth A], JD [auth B], JF [auth G], JH [auth H], JK [auth a], JL [auth a], JM [auth b], JN [auth b], KB [auth A], KD [auth B], KF [auth G], KH [auth H], KK [auth a], KL [auth a], KM [auth b], KN [auth b], KO [auth l], LA [auth A], LB [auth A], LD [auth B], LF [auth G], LH [auth H], LK [auth a], LL [auth a], LM [auth b], LN [auth b], LO [auth l], MA [auth A], MB [auth A], MC [auth B], MD [auth B], MF [auth G], MH [auth H], MK [auth a], ML [auth a], MM [auth b], MN [auth b], MO [auth l], NA [auth A], NB [auth A], NC [auth B], ND [auth B], NH [auth H], NJ [auth T], NK [auth a], NL [auth a], NM [auth b], OA [auth A], OB [auth A], OC [auth B], OD [auth B], OH [auth H], OK [auth a], OM [auth b], ON [auth b], PA [auth A], PB [auth A], PC [auth B], PD [auth B], PF [auth G], PH [auth H], PJ [auth U], PK [auth a], PM [auth b], PN [auth b], QA [auth A], QB [auth A], QC [auth B], QD [auth B], QF [auth G], QH [auth H], QJ [auth U], QK [auth a], QM [auth b], RA [auth A], RB [auth A], RC [auth B], RD [auth B], RF [auth G], RH [auth H], RJ [auth U], RK [auth a], RM [auth b], RO [auth x], SA [auth A], SB [auth A], SC [auth B], SE [auth G], SF [auth G], SH [auth H], SK [auth a], SM [auth b], TA [auth A], TB [auth A], TC [auth B], TD [auth B], TE [auth G], TF [auth G], TG [auth H], TH [auth H], TK [auth a], TM [auth b], UA [auth A], UB [auth A], UC [auth B], UD [auth B], UE [auth G], UF [auth G], UG [auth H], UH [auth H], UM [auth b], VA [auth A], VB [auth A], VC [auth B], VD [auth B], VE [auth G], VF [auth G], VG [auth H], VH [auth H], VM [auth b], WA [auth A], WB [auth A], WC [auth B], WD [auth B], WE [auth G], WF [auth G], WG [auth H], WH [auth H], WJ [auth W], WK [auth a], WM [auth b], XA [auth A], XB [auth A], XC [auth B], XD [auth B], XE [auth G], XF [auth G], XG [auth H], XH [auth H], XJ [auth X], XK [auth a], XM [auth b], YA [auth A], YB [auth A], YC [auth B], YD [auth B], YE [auth G], YF [auth G], YG [auth H], YH [auth H], YK [auth a], YM [auth b], ZA [auth A], ZB [auth A], ZC [auth B], ZE [auth G], ZF [auth G], ZG [auth H], ZI [auth K], ZJ [auth a], ZK [auth a], ZM [auth b]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0	KA [auth A], RE [auth G], YJ [auth a]	CHLOROPHYLL A ISOMER C55 H72 Mg N4 O5 VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG	BO [auth b], GJ [auth L], HO [auth i], JC [auth A], MJ [auth R], NE [auth B], PO [auth l], QG [auth G], UI [auth H], UJ [auth U], XL [auth a], YI [auth I]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	CO [auth b], IC [auth A], OE [auth B], PG [auth G], VI [auth H], WL [auth a]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR	AO [auth b], CC [auth A], DC [auth A], DE [auth B], EC [auth A], EE [auth B], EJ [auth L], FC [auth A], FE [auth B], FJ [auth L], FO [auth i], GC [auth A], GE [auth B], GO [auth i], HC [auth A], HE [auth B], HJ [auth M], IE [auth B], JE [auth B], JG [auth G], KE [auth B], KG [auth G], KI [auth H], KJ [auth R], LE [auth B], LG [auth G], LI [auth H], LJ [auth R], ME [auth B], MG [auth G], MI [auth H], NG [auth G], NI [auth H], NO [auth l], OG [auth G], OI [auth H], OO [auth l], PI [auth H], QI [auth H], QL [auth a], QO [auth m], RI [auth H], RL [auth a], RN [auth b], SI [auth H], SJ [auth U], SL [auth a], SN [auth b], TI [auth H], TJ [auth U], TL [auth a], TN [auth b], UL [auth a], UN [auth b], VJ [auth V], VL [auth a], VN [auth b], WI [auth I], WN [auth b], XI [auth I], XN [auth b], YN [auth b], ZN [auth b]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	KC [auth A], LC [auth A], RG [auth G], SG [auth G], YL [auth a], ZL [auth a]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN	AC [auth A], CE [auth B], HG [auth G], JI [auth H], OL [auth a], QN [auth b]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4	BC [auth A], DO [auth c], EO [auth c], IG [auth G], IJ [auth N], JJ [auth N], PE [auth C], PL [auth a], QE [auth C]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
CA	AJ [auth L], JO [auth l], OJ [auth U]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	GA [auth k], K, T	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Gisriel, C.J., Shen, G., Kurashov, V., Ho, M., Zhang, S., Williams, D., Golbeck, J.H., Fromme, P., Bryant, D.A.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1613022
National Science Foundation (NSF, United States)	United States	1531991
Department of Energy (DOE, United States)	United States	DE-SC 0001035
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	P41-GM103311

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 2.0: 2020-02-26
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
• Version 3.0: 2024-10-23
  Changes: Data collection, Database references, Non-polymer description, Refinement description, Structure summary
• Version 4.0: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary