9AU4 | pdb_00009au4

Cryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain

• PDB DOI: https://doi.org/10.2210/pdb9AU4/pdb
• EM Map EMD-43843: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Synechocystis sp. PCC 6803
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-02-28 Released: 2024-12-25 
• Deposition Author(s): Gisriel, C.J., Vasily, K., Iwig, D.F., Russell, B.P., Vinyard, D.J., Golbeck, J.H., Brudvig, G.W., Lakshmi, K.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain.

Gisriel, C.J., Kurashov, V., Iwig, D.F., Russell, B.P., Vinyard, D.J., Brudvig, G.W., Golbeck, J.H., Lakshmi, K.V.

(2024) Sci Adv 10: eadp4937-eadp4937

• PubMed: 39612342 
• DOI: https://doi.org/10.1126/sciadv.adp4937
• Primary Citation of Related Structures:  
  9AU4


• PubMed Abstract: 
  

  Photosystem I (PS I) is a light-driven oxidoreductase responsible for converting photons into chemical bond energy. Its application for renewable energy was revolutionized by the creation of the MenB deletion (Δ menB ) variant in the cyanobacterium Synechocystis sp. PCC 6803, in which phylloquinone is replaced by plastoquinone-9 with a low binding affinity. This permits its exchange with exogenous quinones covalently coupled to dihydrogen catalysts that bind with high affinity, thereby converting PS I into a stable solar fuel catalyst. Here, we reveal the 2.03-Å-resolution cryo-EM structure of a recent MenB variant of PS I. The quinones and their binding environment are analyzed in the context of previous biophysical data, thereby enabling a protocol to solve future PS I hybrids and constructs from this genetically tractable cyanobacterium.

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Organizational Affiliation: 
• Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Department of Chemistry and Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA 16802, USA.
Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA.
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 33-mer - A3B3C3D3E3F3G3H3I3J3K3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 33-mer - A6B3C3D3E3F3G3H3I3J3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,077.74 kDa 
• Atom Count: 73,866 
• Modeled Residue Count: 6,678 
• Deposited Residue Count: 6,900 
• Unique protein chains: 11

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A [auth G], L [auth a], W [auth A]	751	Synechocystis sp. PCC 6803	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P29254 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P29254  Go to UniProtKB:  P29254

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A2	B [auth H], M [auth b], X [auth B]	730	Synechocystis sp. PCC 6803	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P29255 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P29255  Go to UniProtKB:  P29255

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	C [auth N], N [auth c], Y [auth C]	81	Synechocystis sp. PCC 6803	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P32422 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P32422  Go to UniProtKB:  P32422

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit II	D [auth O], O [auth d], Z [auth D]	141	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for P19569 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P19569  Go to UniProtKB:  P19569

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV	AA [auth E], E [auth P], P [auth e]	74	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12975 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P12975  Go to UniProtKB:  P12975

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit III	BA [auth F], F [auth Q], Q [auth f]	165	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P29256 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P29256  Go to UniProtKB:  P29256

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VIII	CA [auth I], G [auth R], R [auth i]	40	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q55330 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55330  Go to UniProtKB:  Q55330

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	DA [auth J], H [auth S], S [auth j]	40	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q55329 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55329  Go to UniProtKB:  Q55329

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit PsaK 2	EA [auth K], I [auth T], T [auth k]	90	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P74564 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P74564  Go to UniProtKB:  P74564

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XI	FA [auth L], J [auth U], U [auth l]	157	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P37277 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P37277  Go to UniProtKB:  P37277

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XII	GA [auth M], K [auth V], V [auth m]	31	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P72986 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P72986  Go to UniProtKB:  P72986

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	GF [auth U], KK [auth l], OP [auth L]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AB [auth G], AD [auth H], AF [auth U], AG [auth a], AI [auth b], AJ [auth b], AL [auth A], AM [auth A], AN [auth B], AO [auth B], BB [auth G], BD [auth H], BF [auth U], BG [auth a], BI [auth b], BJ [auth b], BK [auth k], BL [auth A], BM [auth A], BN [auth B], BO [auth B], BP [auth J], CB [auth G], CD [auth H], CF [auth U], CG [auth a], CI [auth b], CK [auth l], CL [auth A], CN [auth B], CO [auth B], CP [auth J], DB [auth G], DD [auth H], DG [auth a], DI [auth b], DL [auth A], DN [auth B], DO [auth B], EB [auth G], EC [auth G], ED [auth H], EG [auth a], EI [auth b], EK [auth l], EL [auth A], EN [auth B], EO [auth B], FB [auth G], FC [auth G], FD [auth H], FG [auth a], FI [auth b], FK [auth l], FL [auth A], FN [auth B], FO [auth B], FP [auth K], GB [auth G], GD [auth H], GG [auth a], GI [auth b], GK [auth l], GL [auth A], GN [auth B], GO [auth B], GP [auth L], HA [auth G], HB [auth G], HD [auth H], HG [auth a], HI [auth b], HL [auth A], HN [auth B], IA [auth G], IB [auth G], IC [auth G], ID [auth H], IE [auth H], IG [auth a], IH [auth a], II [auth b], IL [auth A], IN [auth B], IP [auth L], JA [auth G], JB [auth G], JC [auth H], JD [auth H], JG [auth a], JH [auth a], JI [auth b], JL [auth A], JN [auth B], JP [auth L], KA [auth G], KB [auth G], KC [auth H], KD [auth H], KG [auth a], KI [auth b], KL [auth A], KN [auth B], KP [auth L], LA [auth G], LB [auth G], LC [auth H], LD [auth H], LF [auth a], LG [auth a], LI [auth b], LL [auth A], LN [auth B], MA [auth G], MB [auth G], MC [auth H], MD [auth H], ME [auth Q], MF [auth a], MG [auth a], MH [auth a], MI [auth b], MJ [auth b], ML [auth A], MM [auth A], MN [auth B], NA [auth G], NB [auth G], NC [auth H], ND [auth H], NF [auth a], NG [auth a], NH [auth b], NI [auth b], NL [auth A], NM [auth A], NN [auth B], OA [auth G], OB [auth G], OC [auth H], OD [auth H], OE [auth Q], OF [auth a], OG [auth a], OH [auth b], OI [auth b], OL [auth A], ON [auth B], PA [auth G], PB [auth G], PC [auth H], PD [auth H], PE [auth Q], PF [auth a], PG [auth a], PH [auth b], PI [auth b], PK [auth A], PL [auth A], PN [auth B], QA [auth G], QB [auth G], QC [auth H], QD [auth H], QF [auth a], QG [auth a], QH [auth b], QI [auth b], QJ [auth f], QK [auth A], QL [auth A], QM [auth A], QN [auth B], RA [auth G], RB [auth G], RC [auth H], RD [auth H], RF [auth a], RG [auth a], RH [auth b], RI [auth b], RK [auth A], RL [auth A], RM [auth B], RN [auth B], SA [auth G], SB [auth G], SC [auth H], SD [auth H], SF [auth a], SG [auth a], SH [auth b], SI [auth b], SJ [auth f], SK [auth A], SL [auth A], SM [auth B], SN [auth B], TA [auth G], TB [auth G], TC [auth H], TD [auth H], TE [auth S], TF [auth a], TG [auth a], TH [auth b], TI [auth b], TJ [auth f], TK [auth A], TL [auth A], TM [auth B], TN [auth B], UA [auth G], UC [auth H], UD [auth H], UE [auth S], UF [auth a], UG [auth a], UH [auth b], UI [auth b], UK [auth A], UL [auth A], UM [auth B], UN [auth B], UO [auth F], VA [auth G], VC [auth H], VD [auth H], VF [auth a], VG [auth a], VH [auth b], VI [auth b], VK [auth A], VL [auth A], VM [auth B], VN [auth B], WA [auth G], WC [auth H], WD [auth H], WF [auth a], WG [auth a], WH [auth b], WI [auth b], WK [auth A], WL [auth A], WM [auth B], WN [auth B], WO [auth F], XA [auth G], XC [auth H], XD [auth H], XE [auth T], XF [auth a], XG [auth a], XH [auth b], XI [auth b], XJ [auth j], XK [auth A], XL [auth A], XM [auth B], XN [auth B], XO [auth F], YA [auth G], YC [auth H], YE [auth U], YF [auth a], YH [auth b], YI [auth b], YJ [auth j], YK [auth A], YL [auth A], YM [auth B], YN [auth B], ZA [auth G], ZC [auth H], ZF [auth a], ZH [auth b], ZI [auth b], ZK [auth A], ZL [auth A], ZM [auth B], ZN [auth B]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD	FF [auth U], JF [auth V], JK [auth l], NK [auth m], NP [auth L], QP [auth M]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	BC [auth G], DC [auth G], DE [auth H], FH [auth a], HH [auth a], HJ [auth b], JM [auth A], LM [auth A], MO [auth B]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	AC [auth G], CC [auth G], EE [auth H], EH [auth a], GH [auth a], IJ [auth b], IM [auth A], KF [auth V], KM [auth A], NO [auth B], OK [auth m], RP [auth M]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
ZEX	HE [auth H], LJ [auth b], QE [auth Q], QO [auth B], UJ [auth f], YO [auth F]	(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol C40 H56 O2 YRMDXLDAZBQLBK-WIHRHFSMSA-N
EQ3	GE [auth H], KJ [auth b], PO [auth B]	(3'R)-3'-hydroxy-beta,beta-caroten-4-one C40 H54 O2 ZRCXVNZZDQGBQT-BANQPSJHSA-N
45D	GC [auth G], KH [auth a], OM [auth A]	beta,beta-carotene-4,4'-dione C40 H52 O2 FDSDTBUPSURDBL-DKLMTRRASA-N
ECH	DJ [auth b], IF [auth V], IO [auth B], MK [auth m], SP [auth M], ZD [auth H]	beta,beta-caroten-4-one C40 H54 O QXNWZXMBUKUYMD-QQGJMDNJSA-N
BCR	AE [auth H], AH [auth a], AK [auth k], AP [auth J], BE [auth H], BH [auth a], CE [auth H], CH [auth a], CJ [auth b], DF [auth U], DH [auth a], DP [auth J], EF [auth U], EJ [auth b], EM [auth A], EP [auth K], FJ [auth b], FM [auth A], GJ [auth b], GM [auth A], HK [auth l], HM [auth A], HO [auth B], IK [auth l], JO [auth B], KO [auth B], LO [auth B], LP [auth L], MP [auth L], NE [auth Q], RE [auth R], RJ [auth f], SE [auth S], VE [auth S], VJ [auth i], VO [auth F], WB [auth G], WE [auth T], WJ [auth j], XB [auth G], YB [auth G], YD [auth H], ZB [auth G], ZJ [auth j], ZO [auth I]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	HF [auth U], LK [auth l], PP [auth L]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
A1AGD	CM [auth A], JE [auth H], NJ [auth b], RO [auth B], UB [auth G], YG [auth a]	2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione C28 H46 O2 ZPVFWTSVFVOTQH-HAVVHWLPSA-N
SF4	DM [auth A], KE [auth N], LE [auth N], OJ [auth c], PJ [auth c], SO [auth C], TO [auth C], VB [auth G], ZG [auth a]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
CA	DK [auth l], FE [auth H], HP [auth L], JJ [auth b], OO [auth B], ZE [auth U]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	HC [auth G], LH [auth a], PM [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Gisriel, C.J., Vasily, K., Iwig, D.F., Russell, B.P., Vinyard, D.J., Golbeck, J.H., Brudvig, G.W., Lakshmi, K.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	K99GM140174
Department of Energy (DOE, United States)	United States	DE-FG02-07ER15903
Department of Energy (DOE, United States)	United States	DE-SC0010575
Department of Energy (DOE, United States)	United States	DE-FG02-05ER15646
Department of Energy (DOE, United States)	United States	DE-SC0020119

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release