7QCO

The structure of Photosystem I tetramer from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium

• PDB DOI: https://doi.org/10.2210/pdb7QCO/pdb
• Entry: 7QCO supersedes: 6QWJ
• EM Map EMD-13898: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Chroococcidiopsis sp. TS-821
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2021-11-24 Released: 2022-04-06 
• Deposition Author(s): Semchonok, D.A., Mondal, J., Cooper, J.C., Schlum, K., Li, M., Amin, M., Sorzano, C.O.S., Ramirez-Aportela, E., Kastritis, P.L., Boekema, E.J., Guskov, A., Bruce, B.D.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6QWJ

Literature

Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium.

Semchonok, D.A., Mondal, J., Cooper, C.J., Schlum, K., Li, M., Amin, M., Sorzano, C.O.S., Ramirez-Aportela, E., Kastritis, P.L., Boekema, E.J., Guskov, A., Bruce, B.D.

(2022) Plant Commun 3: 100248-100248

• PubMed: 35059628 
• DOI: https://doi.org/10.1016/j.xplc.2021.100248
• Primary Citation of Related Structures:  
  7QCO


• PubMed Abstract: 
  

  Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric form of PSI in plants and algae. The tetrameric organization raises questions about its structural, physiological, and evolutionary significance. Here we report the ∼3.72 Å resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic, unicellular cyanobacterium Chroococcidiopsis sp. TS-821. The structure resolves 44 subunits and 448 cofactor molecules. We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization. The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers. Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state. Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.

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Organizational Affiliation: 

Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, the Netherlands.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 44-mer - A4B4C4D4E4F4G4H4I4J4K4 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 44-mer - A8B4C4D4E4F4G4H4I4J4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,441.06 kDa 
• Atom Count: 90,396 
• Modelled Residue Count: 8,812 
• Deposited Residue Count: 9,652 
• Unique protein chains: 11

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A, HA [auth a], L [auth E], W [auth e]	752	Chroococcidiopsis sp. TS-821	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for A0A2S6VGM5 (Chroococcidiopsis sp. TS-821) Explore A0A2S6VGM5  Go to UniProtKB:  A0A2S6VGM5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A2	B, IA [auth b], M [auth G], X [auth g]	737	Chroococcidiopsis sp. TS-821	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for A0A2S6VGS2 (Chroococcidiopsis sp. TS-821) Explore A0A2S6VGS2  Go to UniProtKB:  A0A2S6VGS2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	C, JA [auth c], N [auth H], Y [auth h]	82	Chroococcidiopsis sp. TS-821	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for A0A2S6VD54 (Chroococcidiopsis sp. TS-821) Explore A0A2S6VD54  Go to UniProtKB:  A0A2S6VD54

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit II	D, KA [auth d], O [auth N], Z [auth n]	168	Chroococcidiopsis sp. TS-821	Mutation(s): 0
UniProt
Find proteins for A0A2S6VI21 (Chroococcidiopsis sp. TS-821) Explore A0A2S6VI21  Go to UniProtKB:  A0A2S6VI21

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV	AA [auth v], E [auth V], LA [auth w], P [auth W]	126	Chroococcidiopsis sp. TS-821	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A2S6VHU0 (Chroococcidiopsis sp. TS-821) Explore A0A2S6VHU0  Go to UniProtKB:  A0A2S6VHU0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit III	BA [auth o], F, MA [auth f], Q [auth O]	164	Chroococcidiopsis sp. TS-821	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A2S6VDZ1 (Chroococcidiopsis sp. TS-821) Explore A0A2S6VDZ1  Go to UniProtKB:  A0A2S6VDZ1

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VIII	CA [auth p], G [auth I], NA [auth i], R [auth P]	39	Chroococcidiopsis sp. TS-821	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A2S6VDT4 (Chroococcidiopsis sp. TS-821) Explore A0A2S6VDT4  Go to UniProtKB:  A0A2S6VDT4

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	DA [auth q], H [auth J], OA [auth j], S [auth Q]	49	Chroococcidiopsis sp. TS-821	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for V5JYA2 (Chroococcidiopsis sp. TS-821) Explore V5JYA2  Go to UniProtKB:  V5JYA2

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit PsaK	EA [auth r], I [auth K], PA [auth k], T [auth R]	93	Chroococcidiopsis sp. TS-821	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A2S6V467 (Chroococcidiopsis sp. TS-821) Explore A0A2S6V467  Go to UniProtKB:  A0A2S6V467

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XI	FA [auth s], J [auth L], QA [auth l], U [auth S]	172	Chroococcidiopsis sp. TS-821	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for V5JYE0 (Chroococcidiopsis sp. TS-821) Explore V5JYE0  Go to UniProtKB:  V5JYE0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XII	GA [auth t], K [auth M], RA [auth m], V [auth T]	31	Chroococcidiopsis sp. TS-821	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A2S6V6A8 (Chroococcidiopsis sp. TS-821) Explore A0A2S6V6A8  Go to UniProtKB:  A0A2S6V6A8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLA	AB [auth A], AC [auth A], AD [auth B], AE [auth B], AF [auth L], AG [auth E], AI [auth G], AK [auth e], AL [auth e], AM [auth g], AN [auth g], AP [auth a], AR [auth b], AS [auth f], BB [auth A], BC [auth A], BD [auth B], BE [auth B], BF [auth L], BG [auth E], BI [auth G], BK [auth e], BL [auth e], BM [auth g], BN [auth g], BP [auth a], BQ [auth b], BR [auth b], CB [auth A], CC [auth A], CD [auth B], CE [auth B], CG [auth E], CI [auth G], CK [auth e], CL [auth e], CM [auth g], CN [auth g], CP [auth a], CQ [auth b], CR [auth b], DB [auth A], DC [auth A], DD [auth B], DE [auth B], DG [auth E], DH [auth G], DI [auth G], DJ [auth O], DK [auth e], DL [auth e], DM [auth g], DN [auth g], DO [auth a], DP [auth a], DQ [auth b], DR [auth b], EB [auth A], EC [auth A], ED [auth B], EE [auth B], EG [auth E], EH [auth G], EI [auth G], EK [auth e], EL [auth e], EM [auth g], EN [auth g], EO [auth a], EP [auth a], EQ [auth b], ER [auth b], ES [auth k], FB [auth A], FC [auth A], FD [auth B], FE [auth B], FF [auth E], FG [auth E], FH [auth G], FI [auth G], FK [auth e], FL [auth e], FM [auth g], FO [auth a], FP [auth a], FQ [auth b], FR [auth b], FS [auth l], GB [auth A], GC [auth A], GD [auth B], GE [auth B], GF [auth E], GG [auth E], GH [auth G], GI [auth G], GK [auth e], GL [auth e], GM [auth g], GO [auth a], GP [auth a], GQ [auth b], GR [auth b], HB [auth A], HC [auth A], HD [auth B], HE [auth B], HF [auth E], HG [auth E], HH [auth G], HI [auth G], HJ [auth R], HK [auth e], HM [auth g], HO [auth a], HP [auth a], HQ [auth b], HR [auth b], HS [auth l], IB [auth A], IC [auth A], ID [auth B], IF [auth E], IG [auth E], IH [auth G], II [auth G], IK [auth e], IM [auth g], IO [auth a], IP [auth a], IQ [auth b], IR [auth b], IS [auth l], JB [auth A], JC [auth A], JD [auth B], JF [auth E], JG [auth E], JH [auth G], JI [auth G], JK [auth e], JM [auth g], JO [auth a], JP [auth a], JQ [auth b], JR [auth b], JS [auth l], KB [auth A], KC [auth A], KD [auth B], KF [auth E], KG [auth E], KH [auth G], KI [auth G], KJ [auth S], KK [auth e], KM [auth g], KO [auth a], KP [auth a], KQ [auth b], KR [auth b], LB [auth A], LD [auth B], LF [auth E], LG [auth E], LH [auth G], LI [auth G], LJ [auth S], LK [auth e], LM [auth g], LO [auth a], LP [auth a], LQ [auth b], LR [auth b], MB [auth A], MD [auth B], MF [auth E], MG [auth E], MH [auth G], MI [auth G], MK [auth e], MM [auth g], MO [auth a], MP [auth a], MQ [auth b], MR [auth b], NB [auth A], ND [auth B], NF [auth E], NG [auth E], NH [auth G], NI [auth G], NJ [auth S], NK [auth e], NM [auth g], NO [auth a], NP [auth a], NQ [auth b], NR [auth b], OB [auth A], OD [auth B], OF [auth E], OG [auth E], OH [auth G], OI [auth G], OK [auth e], OL [auth e], OM [auth g], OO [auth a], OP [auth a], OQ [auth b], OR [auth b], PB [auth A], PD [auth B], PF [auth E], PG [auth E], PH [auth G], PI [auth G], PK [auth e], PL [auth g], PM [auth g], PN [auth o], PO [auth a], PP [auth a], PQ [auth b], QB [auth A], QD [auth B], QF [auth E], QG [auth E], QH [auth G], QI [auth G], QK [auth e], QL [auth g], QM [auth g], QO [auth a], QP [auth a], QQ [auth b], RB [auth A], RD [auth B], RF [auth E], RG [auth E], RH [auth G], RI [auth G], RJ [auth e], RK [auth e], RL [auth g], RM [auth g], RO [auth a], RP [auth a], RQ [auth b], SB [auth A], SC [auth A], SD [auth B], SE [auth F], SF [auth E], SG [auth E], SH [auth G], SJ [auth e], SK [auth e], SM [auth g], SO [auth a], SP [auth a], SQ [auth b], TB [auth A], TC [auth B], TD [auth B], TF [auth E], TG [auth E], TH [auth G], TJ [auth e], TK [auth e], TL [auth g], TM [auth g], TN [auth r], TO [auth a], TQ [auth b], UA [auth A], UB [auth A], UC [auth B], UD [auth B], UF [auth E], UG [auth E], UH [auth G], UJ [auth e], UK [auth e], UL [auth g], UM [auth g], UN [auth r], UO [auth a], UQ [auth b], VA [auth A], VB [auth A], VD [auth B], VF [auth E], VG [auth E], VH [auth G], VJ [auth e], VK [auth e], VL [auth g], VM [auth g], VO [auth a], VQ [auth b], WA [auth A], WB [auth A], WC [auth B], WD [auth B], WE [auth K], WF [auth E], WG [auth E], WH [auth G], WJ [auth e], WK [auth e], WL [auth g], WM [auth g], WN [auth s], WO [auth a], WQ [auth b], XA [auth A], XB [auth A], XC [auth B], XD [auth B], XE [auth K], XF [auth E], XH [auth G], XJ [auth e], XK [auth e], XL [auth g], XM [auth g], XN [auth s], XO [auth a], XQ [auth b], YA [auth A], YB [auth A], YC [auth B], YD [auth B], YF [auth E], YH [auth G], YJ [auth e], YK [auth e], YL [auth g], YM [auth g], YO [auth a], YQ [auth b], ZA [auth A], ZB [auth A], ZC [auth B], ZD [auth B], ZE [auth L], ZF [auth E], ZH [auth G], ZJ [auth e], ZK [auth e], ZL [auth g], ZM [auth g], ZN [auth s], ZO [auth a], ZP [auth a], ZQ [auth b]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
LHG	AO [auth a], PJ [auth e], QJ [auth e], SA [auth A], TA [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR	AH [auth E], AQ [auth a], BH [auth E], BJ [auth O], BO [auth a], BS [auth i], CF [auth L], CH [auth E], CJ [auth O], CO [auth a], CS [auth j], DF [auth E], DS [auth k], EF [auth E], EJ [auth P], FJ [auth Q], GJ [auth R], GN [auth g], GS [auth l], HN [auth g], IJ [auth S], IL [auth e], IN [auth g], JE [auth B], JJ [auth S], JL [auth e], JN [auth g], KE [auth B], KL [auth e], KN [auth g], KS [auth l], LE [auth B], LL [auth e], LN [auth g], LS [auth m], MC [auth A], ME [auth B], MJ [auth S], ML [auth e], NC [auth A], NE [auth B], NL [auth e], OC [auth A], OE [auth B], OJ [auth T], ON [auth o], PC [auth A], QC [auth A], QN [auth p], QR [auth b], RC [auth A], RE [auth F], RN [auth q], RR [auth b], SN [auth q], SR [auth b], TE [auth I], TI [auth G], TR [auth b], UE [auth J], UI [auth G], UR [auth b], VE [auth J], VI [auth G], VN [auth s], VP [auth a], VR [auth b], WI [auth G], WP [auth a], XI [auth G], XP [auth a], YE [auth L], YI [auth G], YN [auth s], YP [auth a], YR [auth f], ZG [auth E], ZR [auth f]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
PQN	FN [auth g], HL [auth e], IE [auth B], LC [auth A], PR [auth b], SI [auth G], UP [auth a], YG [auth E]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4	AJ [auth H], MN [auth h], NN [auth h], PE [auth C], QE [auth C], SL [auth g], TP [auth a], VC [auth B], WR [auth c], XG [auth E], XR [auth c], ZI [auth H]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.14
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Semchonok, D.A., Mondal, J., Cooper, J.C., Schlum, K., Li, M., Amin, M., Sorzano, C.O.S., Ramirez-Aportela, E., Kastritis, P.L., Boekema, E.J., Guskov, A., Bruce, B.D.
• This entry supersedes: 6QWJ

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DGE-0801470
National Science Foundation (NSF, United States)	United States	EPS-1004083
National Science Foundation (NSF, United States)	United States	2017219379

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release