6NWA

The structure of the photosystem I IsiA super-complex

• PDB DOI: https://doi.org/10.2210/pdb6NWA/pdb
• EM Map EMD-0524: EMDB EMDataResource

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


• Deposited: 2019-02-06 Released: 2019-05-29 
• Deposition Author(s): Toporik, H., Li, J., Williams, D., Chiu, P.L., Mazor, Y.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The structure of the stress-induced photosystem I-IsiA antenna supercomplex.

Toporik, H., Li, J., Williams, D., Chiu, P.L., Mazor, Y.

(2019) Nat Struct Mol Biol 26: 443-449

• PubMed: 31133699 
• DOI: https://doi.org/10.1038/s41594-019-0228-8
• Primary Citation of Related Structures:  
  6NWA


• PubMed Abstract: 
  

  Photochemical conversion in oxygenic photosynthesis takes place in two large protein-pigment complexes named photosystem II and photosystem I (PSII and PSI, respectively). Photosystems associate with antennae in vivo to increase the size of photosynthetic units to hundreds or thousands of pigments. Regulation of the interactions between antennae and photosystems allows photosynthetic organisms to adapt to their environment. In low-iron environments, cyanobacteria express IsiA, a PSI antenna, critical to their survival. Here we describe the structure of the PSI-IsiA complex isolated from the mesophilic cyanobacterium Synechocystis sp. PCC 6803. This 2-MDa photosystem-antenna supercomplex structure reveals more than 700 pigments coordinated by 51 subunits, as well as the mechanisms facilitating the self-assembly and association of IsiA with multiple PSI assemblies.

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Organizational Affiliation: 

School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 51-mer - A18B3C3D3E3F3G3H3I3J3K3L3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 51-mer - A18B6C3D3E3F3G3H3I3J3K3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2,055.66 kDa 
• Atom Count: 137,509 
• Modelled Residue Count: 12,666 
• Deposited Residue Count: 13,047 
• Unique protein chains: 12

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A, DA [auth H], Q [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 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, EA [auth G], R [auth b]	731	Synechocystis sp. PCC 6803	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P29255 (Synechocystis sp. (strain 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, VA [auth c], WA [auth N]	81	Synechocystis sp. PCC 6803	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P32422 (Synechocystis sp. (strain 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, FA [auth O], S [auth d]	141	Synechocystis sp. PCC 6803	Mutation(s): 0
UniProt
Find proteins for P19569 (Synechocystis sp. (strain 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	E, PA [auth e], QA [auth P]	74	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12975 (Synechocystis sp. (strain 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	F, RA [auth f], SA [auth Q]	165	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P29256 (Synechocystis sp. (strain 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	G [auth I], GA [auth R], T [auth i]	40	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q55330 (Synechocystis sp. (strain 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	H [auth J], TA [auth j], UA [auth S]	40	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q55329 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q55329  Go to UniProtKB:  Q55329

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XI	HA [auth U], I [auth L], V [auth l]	157	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P37277 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P37277  Go to UniProtKB:  P37277

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XII	IA [auth V], J [auth M], W [auth m]	31	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P72986 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P72986  Go to UniProtKB:  P72986

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron stress-induced chlorophyll-binding protein	AA [auth q], BA [auth r], CA [auth h], JA [auth t], K [auth W], KA [auth u], L [auth X], LA [auth s], M [auth Y], MA [auth w], N [auth Z], NA [auth x], O [auth g], OA [auth v], P [auth y], X [auth n], Y [auth o], Z [auth p]	342	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q55274 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q55274  Go to UniProtKB:  Q55274

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit PsaK 1	U [auth k], XA [auth K], YA [auth T]	86	Synechocystis sp. PCC 6803	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P72712 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P72712  Go to UniProtKB:  P72712

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLA	AAA [auth u], ABA [auth s], AC [auth A], ADA [auth v], AE [auth B], AG [auth W], AH [auth X], AI [auth Y], AK [auth y], AL [auth a], AM [auth a], AO [auth b], AQ [auth n], AR [auth p], AS [auth q], AT [auth r], AU [auth h], AV [auth H], AW [auth H], AX [auth G], AY [auth G], AZ [auth t], BAA [auth u], BBA [auth s], BC [auth A], BDA [auth v], BE [auth B], BG [auth W], BH [auth X], BI [auth Y], BK [auth y], BL [auth a], BM [auth a], BO [auth b], BQ [auth n], BR [auth p], BS [auth q], BT [auth r], BU [auth h], BV [auth H], BW [auth H], BX [auth G], BY [auth G], BZ [auth t], CAA [auth u], CC [auth A], CCA [auth x], CDA [auth v], CE [auth B], CG [auth W], CH [auth X], CI [auth Y], CK [auth y], CL [auth a], CM [auth a], CN [auth b], CO [auth b], CP [auth k], CQ [auth n], CR [auth p], CS [auth q], CT [auth r], CU [auth h], CV [auth H], CW [auth H], CX [auth G], CY [auth G], CZ [auth t], DAA [auth u], DB [auth A], DC [auth A], DCA [auth x], DDA [auth v], DE [auth B], DEA [auth S], DG [auth W], DH [auth X], DI [auth Y], DK [auth y], DL [auth a], DM [auth a], DN [auth b], DO [auth b], DR [auth p], DS [auth q], DT [auth r], DV [auth H], DW [auth H], DX [auth G], DY [auth G], DZ [auth t], EAA [auth u], EB [auth A], EC [auth A], ECA [auth x], EDA [auth v], EE [auth B], EEA [auth S], EG [auth W], EH [auth X], EJ [auth g], EK [auth y], EL [auth a], EM [auth a], EN [auth b], EO [auth b], EP [auth l], ER [auth p], ES [auth q], ET [auth r], EV [auth H], EX [auth G], EZ [auth t], FAA [auth u], FB [auth A], FC [auth A], FCA [auth x], FDA [auth v], FE [auth B], FG [auth W], FH [auth X], FJ [auth g], FK [auth y], FL [auth a], FM [auth a], FN [auth b], FO [auth b], FP [auth l], FQ [auth o], FR [auth p], FS [auth q], FT [auth r], FV [auth H], FX [auth G], FZ [auth t], GAA [auth u], GB [auth A], GC [auth A], GCA [auth x], GDA [auth v], GE [auth B], GF [auth F], GG [auth W], GH [auth X], GJ [auth g], GK [auth y], GL [auth a], GM [auth a], GN [auth b], GO [auth b], GP [auth l], GQ [auth o], GR [auth p], GS [auth q], GT [auth r], GV [auth H], GX [auth G], GZ [auth t], HB [auth A], HBA [auth w], HC [auth A], HCA [auth x], HD [auth B], HDA [auth v], HE [auth B], HF [auth F], HG [auth W], HH [auth X], HJ [auth g], HK [auth y], HL [auth a], HM [auth a], HN [auth b], HO [auth b], HQ [auth o], HR [auth p], HS [auth q], HT [auth r], HV [auth H], HX [auth G], HZ [auth t], IB [auth A], IBA [auth w], IC [auth A], ICA [auth x], ID [auth B], IDA [auth v], IE [auth B], IG [auth W], IH [auth X], IJ [auth g], IK [auth y], IL [auth a], IM [auth a], IN [auth b], IO [auth b], IQ [auth o], IR [auth p], IS [auth q], IV [auth H], IX [auth G], IZ [auth t], JB [auth A], JBA [auth w], JC [auth A], JCA [auth x], JD [auth B], JDA [auth v], JE [auth B], JG [auth W], JI [auth Z], JJ [auth g], JK [auth y], JL [auth a], JM [auth a], JN [auth b], JO [auth b], JQ [auth o], JR [auth p], JS [auth q], JV [auth H], JX [auth G], JZ [auth t], KB [auth A], KBA [auth w], KC [auth A], KCA [auth x], KD [auth B], KDA [auth v], KE [auth B], KG [auth W], KI [auth Z], KJ [auth g], KK [auth y], KL [auth a], KM [auth a], KN [auth b], KO [auth b], KQ [auth o], KR [auth p], KS [auth q], KV [auth H], KX [auth G], KZ [auth t], LAA [auth s], LB [auth A], LBA [auth w], LC [auth A], LCA [auth x], LD [auth B], LDA [auth v], LE [auth B], LG [auth W], LI [auth Z], LJ [auth g], LK [auth y], LL [auth a], LM [auth a], LN [auth b], LO [auth b], LQ [auth o], LR [auth p], LS [auth q], LU [auth H], LV [auth H], LX [auth G], LZ [auth t], MAA [auth s], MB [auth A], MBA [auth w], MC [auth A], MCA [auth x], MD [auth B], MDA [auth v], ME [auth B], MEA [auth K], MF [auth J], MG [auth W], MI [auth Z], MJ [auth g], MK [auth y], ML [auth a], MM [auth a], MN [auth b], MO [auth b], MP [auth n], MQ [auth o], MR [auth p], MS [auth q], MT [auth h], MU [auth H], MV [auth H], MX [auth G], MZ [auth t], NAA [auth s], NB [auth A], NBA [auth w], NC [auth A], NCA [auth x], ND [auth B], NDA [auth v], NE [auth B], NF [auth J], NG [auth W], NH [auth Y], NI [auth Z], NJ [auth g], NK [auth y], NL [auth a], NM [auth a], NN [auth b], NO [auth b], NP [auth n], NQ [auth o], NR [auth p], NT [auth h], NU [auth H], NV [auth H], NX [auth G], NZ [auth t], OAA [auth s], OB [auth A], OBA [auth w], OC [auth A], OCA [auth x], OD [auth B], OE [auth B], OEA [auth T], OG [auth W], OH [auth Y], OI [auth Z], OJ [auth g], OK [auth y], OL [auth a], OM [auth a], ON [auth b], OO [auth b], OP [auth n], OQ [auth o], OR [auth p], OT [auth h], OU [auth H], OV [auth H], OX [auth G], PAA [auth s], PB [auth A], PBA [auth w], PC [auth A], PCA [auth x], PD [auth B], PE [auth B], PG [auth W], PH [auth Y], PI [auth Z], PJ [auth g], PK [auth y], PL [auth a], PM [auth a], PN [auth b], PO [auth b], PP [auth n], PQ [auth o], PR [auth p], PT [auth h], PU [auth H], PV [auth H], PW [auth G], PX [auth G], PY [auth U], QAA [auth s], QB [auth A], QBA [auth w], QC [auth A], QCA [auth x], QD [auth B], QE [auth B], QH [auth Y], QI [auth Z], QJ [auth g], QL [auth a], QM [auth a], QN [auth b], QO [auth b], QP [auth n], QQ [auth o], QR [auth p], QT [auth h], QU [auth H], QV [auth H], QW [auth G], QX [auth G], QY [auth U], QZ [auth u], RAA [auth s], RB [auth A], RBA [auth w], RC [auth A], RCA [auth x], RD [auth B], RE [auth B], RF [auth L], RH [auth Y], RI [auth Z], RJ [auth g], RL [auth a], RN [auth b], RP [auth n], RQ [auth o], RS [auth r], RT [auth h], RU [auth H], RV [auth H], RW [auth G], RX [auth G], RY [auth U], RZ [auth u], SAA [auth s], SB [auth A], SBA [auth w], SC [auth A], SCA [auth x], SD [auth B], SDA [auth f], SE [auth B], SF [auth L], SG [auth X], SH [auth Y], SI [auth Z], SJ [auth g], SL [auth a], SN [auth b], SP [auth n], SQ [auth o], SS [auth r], ST [auth h], SU [auth H], SV [auth H], SW [auth G], SX [auth G], SZ [auth u], TAA [auth s], TB [auth A], TBA [auth w], TC [auth A], TD [auth B], TDA [auth f], TE [auth B], TF [auth L], TG [auth X], TH [auth Y], TI [auth Z], TJ [auth g], TL [auth a], TN [auth b], TP [auth n], TQ [auth o], TS [auth r], TT [auth h], TU [auth H], TV [auth H], TW [auth G], TX [auth G], TZ [auth u], UAA [auth s], UB [auth A], UBA [auth w], UC [auth A], UD [auth B], UE [auth B], UG [auth X], UH [auth Y], UI [auth Z], UJ [auth g], UL [auth a], UN [auth b], UP [auth n], UQ [auth o], US [auth r], UT [auth h], UU [auth H], UV [auth H], UW [auth G], UX [auth G], UZ [auth u], VAA [auth s], VB [auth A], VBA [auth w], VC [auth A], VD [auth B], VDA [auth Q], VE [auth B], VG [auth X], VH [auth Y], VI [auth Z], VL [auth a], VN [auth b], VP [auth n], VQ [auth o], VS [auth r], VT [auth h], VU [auth H], VV [auth H], VW [auth G], VX [auth G], VZ [auth u], WAA [auth s], WB [auth A], WBA [auth w], WD [auth B], WDA [auth Q], WG [auth X], WH [auth Y], WI [auth Z], WL [auth a], WN [auth b], WP [auth n], WR [auth q], WS [auth r], WT [auth h], WU [auth H], WV [auth H], WW [auth G], WX [auth G], WZ [auth u], XAA [auth s], XB [auth A], XBA [auth w], XCA [auth v], XD [auth B], XG [auth X], XH [auth Y], XI [auth Z], XL [auth a], XN [auth b], XP [auth n], XR [auth q], XS [auth r], XT [auth h], XU [auth H], XV [auth H], XW [auth G], XX [auth G], XY [auth t], XZ [auth u], YAA [auth s], YB [auth A], YCA [auth v], YD [auth B], YDA [auth j], YG [auth X], YH [auth Y], YI [auth Z], YK [auth a], YL [auth a], YN [auth b], YP [auth n], YR [auth q], YS [auth r], YT [auth h], YU [auth H], YV [auth H], YW [auth G], YX [auth G], YY [auth t], YZ [auth u], ZAA [auth s], ZB [auth A], ZCA [auth v], ZD [auth B], ZDA [auth j], ZF [auth W], ZG [auth X], ZH [auth Y], ZI [auth Z], ZJ [auth y], ZK [auth a], ZL [auth a], ZN [auth b], ZP [auth n], ZR [auth q], ZS [auth r], ZT [auth h], ZU [auth H], ZV [auth H], ZW [auth G], ZX [auth G], ZY [auth t], ZZ [auth u]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0	CB [auth A], KU [auth H], XK [auth a]	CHLOROPHYLL A ISOMER C55 H72 Mg N4 O5 VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG	AN [auth a], BB [auth A], BN [auth b], ED [auth A], FD [auth A], GBA [auth s], GD [auth B], II [auth Y], JU [auth H], MW [auth H], NW [auth H], OW [auth G], VR [auth p], WK [auth a], ZM [auth a]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	AB [auth A], HU [auth H], IU [auth H], JF [auth I], MY [auth R], UK [auth a], VK [auth a], ZA [auth A], ZO [auth i]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR	ACA [auth w], AD [auth A], AEA [auth j], AF [auth B], AJ [auth Z], AP [auth i], BCA [auth w], BD [auth A], BEA [auth j], BF [auth B], BJ [auth Z], BP [auth i], CBA [auth s], CD [auth A], CEA [auth j], CF [auth B], CJ [auth Z], DBA [auth s], DD [auth A], DF [auth B], DJ [auth Z], DP [auth k], DQ [auth n], DU [auth h], EBA [auth s], EI [auth Y], EQ [auth n], EU [auth h], FBA [auth s], FEA [auth S], FI [auth Y], FU [auth h], FY [auth G], GEA [auth S], GI [auth Y], GU [auth h], GW [auth H], GY [auth G], HAA [auth u], HEA [auth S], HI [auth Y], HP [auth l], HW [auth H], HY [auth G], IAA [auth u], IF [auth F], IP [auth l], IT [auth r], IW [auth H], IY [auth G], JAA [auth u], JH [auth X], JT [auth r], JW [auth H], JY [auth G], KAA [auth u], KF [auth I], KH [auth X], KT [auth r], KW [auth H], KY [auth G], LF [auth I], LH [auth X], LP [auth m], LT [auth r], LW [auth H], LY [auth G], MH [auth X], NEA [auth K], NS [auth q], NY [auth R], ODA [auth v], OF [auth J], OS [auth q], OY [auth R], OZ [auth t], PDA [auth v], PEA [auth T], PF [auth J], PS [auth q], PZ [auth t], QDA [auth v], QF [auth J], QG [auth W], QK [auth y], QS [auth q], RDA [auth v], RG [auth W], RK [auth y], RR [auth p], SK [auth y], SO [auth b], SR [auth p], SY [auth U], TCA [auth x], TK [auth y], TM [auth a], TO [auth b], TR [auth p], TY [auth U], UCA [auth x], UDA [auth f], UF [auth L], UM [auth a], UO [auth b], UR [auth p], VCA [auth x], VF [auth L], VJ [auth g], VM [auth a], VO [auth b], WCA [auth x], WJ [auth g], WM [auth a], WO [auth b], WQ [auth o], WY [auth V], XDA [auth Q], XE [auth B], XJ [auth g], XM [auth a], XO [auth b], XQ [auth o], YBA [auth w], YC [auth A], YE [auth B], YF [auth M], YJ [auth g], YM [auth a], YO [auth b], YQ [auth o], ZBA [auth w], ZC [auth A], ZE [auth B], ZQ [auth o]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	JP [auth l], UY [auth U], WF [auth L]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN	EW [auth H], EY [auth G], RM [auth a], RO [auth b], WC [auth A], WE [auth B]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4	EF [auth C], FF [auth C], FW [auth H], IEA [auth c], JEA [auth c], KEA [auth N], LEA [auth N], SM [auth a], XC [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
CA	KP [auth l], VY [auth U], XF [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX	1.14-3260

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Toporik, H., Li, J., Williams, D., Chiu, P.L., Mazor, Y.

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references
• Version 1.2: 2019-06-19
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Other
• Version 2.0: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Non-polymer description