7DR2

Structure of GraFix PSI tetramer from Cyanophora paradoxa

• PDB DOI: https://doi.org/10.2210/pdb7DR2/pdb
• EM Map EMD-30823: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Cyanophora paradoxa
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2020-12-25 Released: 2022-02-16 
• Deposition Author(s): Kato, K., Nagao, R., Akita, F., Miyazaki, N., Shen, J.R.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes

Kato, K., Nagao, R., Ueno, Y., Yokono, M., Suzuki, T., Jiang, T.Y., Dohmae, N., Akita, F., Akimoto, S., Miyazaki, N., Shen, J.R.

(2022) Biorxiv 

• DOI: https://doi.org/10.1101/2022.01.03.474851

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 42-mer - A4B4C4D4E4F4G4H4I4J4K2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 42-mer - A8B6C4D4E4F4G4H4I2J2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 1,399.74 kDa 
• Atom Count: 89,952 
• Modelled Residue Count: 8,588 
• Deposited Residue Count: 9,506 
• Unique protein chains: 11

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A [auth aA], GA [auth dA], L [auth bA], V [auth cA]	752	Cyanophora paradoxa	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for A0A097PBL3 (Cyanophora paradoxa) Explore A0A097PBL3  Go to UniProtKB:  A0A097PBL3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A2	B [auth aB], HA [auth dB], M [auth bB], W [auth cB]	737	Cyanophora paradoxa	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P48113 (Cyanophora paradoxa) Explore P48113  Go to UniProtKB:  P48113

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	C [auth aC], IA [auth dC], N [auth bC], X [auth cC]	81	Cyanophora paradoxa	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P31173 (Cyanophora paradoxa) Explore P31173  Go to UniProtKB:  P31173

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit II, cyanelle	D [auth aD], JA [auth dD], O [auth bD], Y [auth cD]	220	Cyanophora paradoxa	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9T4W8 (Cyanophora paradoxa) Explore Q9T4W8  Go to UniProtKB:  Q9T4W8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV	E [auth aE], KA [auth dE], P [auth bE], Z [auth cE]	70	Cyanophora paradoxa	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P48114 (Cyanophora paradoxa) Explore P48114  Go to UniProtKB:  P48114

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit III	AA [auth cF], F [auth aF], LA [auth dF], Q [auth bF]	186	Cyanophora paradoxa	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P48115 (Cyanophora paradoxa) Explore P48115  Go to UniProtKB:  P48115

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VIII	BA [auth cI], G [auth aI], MA [auth dI], R [auth bI]	35	Cyanophora paradoxa	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P48116 (Cyanophora paradoxa) Explore P48116  Go to UniProtKB:  P48116

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	CA [auth cJ], H [auth aJ], NA [auth dJ], S [auth bJ]	40	Cyanophora paradoxa	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P48117 (Cyanophora paradoxa) Explore P48117  Go to UniProtKB:  P48117

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit PsaK 1	DA [auth cK], I [auth aK]	157	Cyanophora paradoxa	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XI	EA [auth cL], J [auth aL], OA [auth dL], T [auth bL]	146	Cyanophora paradoxa	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XII	FA [auth cM], K [auth aM], PA [auth dM], U [auth bM]	31	Cyanophora paradoxa	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P48185 (Cyanophora paradoxa) Explore P48185  Go to UniProtKB:  P48185

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-02-16 
Deposition Author(s): Kato, K., Nagao, R., Akita, F., Miyazaki, N., Shen, J.R.

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release