8WM6

The structure of PSI-CAC(L-14)of R.salina at 2.7 angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb8WM6/pdb
• EM Map EMD-37642: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Rhodomonas salina
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-10-03 Released: 2024-05-29 
• Deposition Author(s): Zhang, S.M., Si, L., Li, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Growth phase-dependent reorganization of cryptophyte photosystem I antennae.

Zhang, S., Si, L., Su, X., Zhao, X., An, X., Li, M.

(2024) Commun Biol 7: 560-560

• PubMed: 38734819 
• DOI: https://doi.org/10.1038/s42003-024-06268-5
• Primary Citation of Related Structures:  
  8WM6, 8WMJ, 8WMV, 8WMW, 8WNW


• PubMed Abstract: 
  

  Photosynthetic cryptophytes are eukaryotic algae that utilize membrane-embedded chlorophyll a/c binding proteins (CACs) and lumen-localized phycobiliproteins (PBPs) as their light-harvesting antennae. Cryptophytes go through logarithmic and stationary growth phases, and may adjust their light-harvesting capability according to their particular growth state. How cryptophytes change the type/arrangement of the photosynthetic antenna proteins to regulate their light-harvesting remains unknown. Here we solve four structures of cryptophyte photosystem I (PSI) bound with CACs that show the rearrangement of CACs at different growth phases. We identify a cryptophyte-unique protein, PsaQ, which harbors two chlorophyll molecules. PsaQ specifically binds to the lumenal region of PSI during logarithmic growth phase and may assist the association of PBPs with photosystems and energy transfer from PBPs to photosystems.

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Organizational Affiliation: 

Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 29-mer - A3B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 29-mer - A13B2C2D1E1F1G1H1I1J1K1L1M1N1O1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 988.09 kDa 
• Atom Count: 61,164 
• Modelled Residue Count: 5,216 
• Deposited Residue Count: 6,189 
• Unique protein chains: 27

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A	752	Rhodomonas salina	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for A6MVZ7 (Rhodomonas salina) Explore A6MVZ7  Go to UniProtKB:  A6MVZ7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A2	B	734	Rhodomonas salina	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for A6MVZ6 (Rhodomonas salina) Explore A6MVZ6  Go to UniProtKB:  A6MVZ6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	C	81	Rhodomonas salina	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for A6MVS8 (Rhodomonas salina) Explore A6MVS8  Go to UniProtKB:  A6MVS8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit II	D	141	Rhodomonas salina	Mutation(s): 0
UniProt
Find proteins for A6MVZ1 (Rhodomonas salina) Explore A6MVZ1  Go to UniProtKB:  A6MVZ1

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV	E	64	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MW36 (Rhodomonas salina) Explore A6MW36  Go to UniProtKB:  A6MW36

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit III	F	188	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVU7 (Rhodomonas salina) Explore A6MVU7  Go to UniProtKB:  A6MVU7

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VIII	G [auth I]	36	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVV1 (Rhodomonas salina) Explore A6MVV1  Go to UniProtKB:  A6MVV1

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	H [auth J]	42	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVU6 (Rhodomonas salina) Explore A6MVU6  Go to UniProtKB:  A6MVU6

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XI	I [auth L]	153	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVV8 (Rhodomonas salina) Explore A6MVV8  Go to UniProtKB:  A6MVV8

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XII	J [auth M]	30	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVT4 (Rhodomonas salina) Explore A6MVT4  Go to UniProtKB:  A6MVT4

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaO	K [auth O]	146	Rhodomonas salina	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit PsaK	L [auth K]	87	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVS9 (Rhodomonas salina) Explore A6MVS9  Go to UniProtKB:  A6MVS9

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
chain s	M [auth s]	269	Rhodomonas salina	Mutation(s): 0

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-c	N [auth c]	216	Rhodomonas salina	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-a	O [auth a]	216	Rhodomonas salina	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-b	P [auth b]	223	Rhodomonas salina	Mutation(s): 0

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-h	Q [auth h]	225	Rhodomonas salina	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-f	R [auth m], V [auth f], X [auth j]	212	Rhodomonas salina	Mutation(s): 0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-e	S [auth e]	203	Rhodomonas salina	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-l	T [auth l]	238	Rhodomonas salina	Mutation(s): 0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-k	U [auth k]	241	Rhodomonas salina	Mutation(s): 0

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-i	W [auth i]	218	Rhodomonas salina	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-d	Y [auth d]	213	Rhodomonas salina	Mutation(s): 0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-g	Z [auth g]	255	Rhodomonas salina	Mutation(s): 0

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaR	AA [auth R]	129	Rhodomonas salina	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
cac-n	BA [auth n]	219	Rhodomonas salina	Mutation(s): 0

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaQ	CA [auth Q]	234	Rhodomonas salina	Mutation(s): 0

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	WD [auth B]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AB [auth A], AD [auth B], AF [auth O], AG [auth c], AJ [auth m], AK [auth l], AN [auth j], AP [auth g], AQ [auth Q], BB [auth A], BC [auth A], BD [auth B], BF [auth O], BI [auth h], BK [auth l], BN [auth j], BQ [auth Q], CB [auth A], CC [auth A], CD [auth B], CG [auth c], CI [auth h], CK [auth l], CL [auth k], CN [auth j], DA [auth A], DB [auth A], DD [auth B], DG [auth c], DI [auth h], DK [auth l], DN [auth j], DP [auth R], EA [auth A], EB [auth A], EC [auth A], ED [auth B], EE [auth F], EI [auth h], EK [auth l], EM [auth i], EN [auth j], FA [auth A], FB [auth A], FC [auth A], FD [auth B], FE [auth F], FF [auth O], FI [auth h], FK [auth l], FM [auth i], FN [auth j], FP [auth n], GA [auth A], GB [auth A], GC [auth B], GD [auth B], GF [auth K], GH [auth b], GI [auth h], GK [auth l], GM [auth i], GN [auth j], GO [auth g], GP [auth n], HA [auth A], HB [auth A], HC [auth B], HD [auth B], HH [auth b], HI [auth h], HJ [auth e], HM [auth i], HO [auth g], HP [auth n], IA [auth A], IB [auth A], IC [auth B], ID [auth B], IF [auth K], IH [auth b], II [auth h], IJ [auth e], IK [auth l], IM [auth i], IN [auth j], IO [auth g], IP [auth n], JA [auth A], JB [auth A], JC [auth B], JD [auth B], JH [auth b], JJ [auth e], JM [auth i], JN [auth j], JO [auth g], JP [auth n], KA [auth A], KB [auth A], KC [auth B], KD [auth B], KH [auth b], KJ [auth e], KL [auth f], KM [auth i], KO [auth g], KP [auth n], LA [auth A], LB [auth A], LC [auth B], LD [auth B], LF [auth s], LH [auth b], LJ [auth e], LL [auth f], LM [auth i], LO [auth g], LP [auth n], MA [auth A], MB [auth A], MC [auth B], MD [auth B], ME [auth J], MF [auth s], MH [auth b], MJ [auth e], ML [auth f], MO [auth g], MP [auth n], NA [auth A], NB [auth A], NC [auth B], ND [auth B], NH [auth b], NI [auth h], NJ [auth e], NL [auth f], NM [auth i], NO [auth g], NP [auth n], OA [auth A], OB [auth A], OC [auth B], OD [auth B], OG [auth a], OH [auth b], OI [auth m], OJ [auth e], OL [auth f], OM [auth i], ON [auth d], OO [auth g], OP [auth n], PA [auth A], PB [auth A], PC [auth B], PD [auth B], PF [auth s], PG [auth a], PH [auth b], PI [auth m], PK [auth k], PL [auth f], PN [auth d], PO [auth g], QA [auth A], QB [auth A], QC [auth B], QD [auth B], QG [auth a], QH [auth b], QI [auth m], QJ [auth e], QK [auth k], QL [auth f], QN [auth d], RA [auth A], RB [auth A], RC [auth B], RD [auth B], RE [auth L], RF [auth s], RG [auth a], RH [auth b], RI [auth m], RJ [auth e], RK [auth k], RL [auth f], RN [auth d], RP [auth n], SA [auth A], SC [auth B], SD [auth B], SE [auth L], SF [auth c], SG [auth a], SI [auth m], SK [auth k], SL [auth f], SN [auth d], TA [auth A], TC [auth B], TD [auth B], TE [auth L], TF [auth c], TG [auth a], TI [auth m], TK [auth k], TL [auth f], TN [auth d], TO [auth g], UA [auth A], UC [auth B], UD [auth B], UF [auth c], UG [auth a], UI [auth m], UK [auth k], UN [auth d], VA [auth A], VC [auth B], VF [auth c], VG [auth a], VI [auth m], VK [auth k], VL [auth f], VN [auth d], WA [auth A], WC [auth B], WE [auth L], WF [auth c], WG [auth a], WI [auth m], WK [auth k], WL [auth f], WN [auth d], XA [auth A], XC [auth B], XF [auth c], XG [auth a], XI [auth m], XK [auth k], XM [auth j], YA [auth A], YC [auth B], YF [auth c], YG [auth a], YK [auth k], YM [auth j], ZA [auth A], ZC [auth B], ZF [auth c], ZI [auth m], ZJ [auth l], ZM [auth j], ZN [auth d]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG	AI [auth b], EF [auth O], IE [auth F], KG [auth c], OE [auth J], YE [auth L], YP [auth n], ZP [auth Q]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	CM [auth f], EH [auth a], EO [auth d], FO [auth g], GJ [auth m], IL [auth k], JG [auth c], LG [auth c], MG [auth a], NN [auth j], OK [auth l], PE [auth J], TB [auth A], UB [auth A], UM [auth i], XE [auth L], XJ [auth e], XP [auth n], YH [auth b], ZB [auth A], ZH [auth b], ZO [auth g]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
KC2	AL [auth k], BG [auth c], BL [auth k], HK [auth l], HN [auth j], KF [auth s], MM [auth i], NF [auth s], PJ [auth e], PP [auth n], QO [auth g], QP [auth n], RO [auth g], SO [auth g], UL [auth f], VM [auth i], XN [auth d], YI [auth m], YN [auth d], ZK [auth k]	Chlorophyll c2 C35 H28 Mg N4 O5 QDRBYWCRXZZVLY-QIEHNWLWSA-L
II0 (Subject of Investigation/LOI)	AH [auth a], AO [auth d], BH [auth a], BJ [auth m], BM [auth f], BO [auth d], CF [auth O], CJ [auth m], CO [auth d], DH [auth a], DJ [auth m], DL [auth k], DO [auth d], EG [auth c], EL [auth k], FG [auth c], FJ [auth m], FL [auth k], GG [auth c], HL [auth k], IG [auth c], JK [auth l], JL [auth k], KI [auth h], KK [auth l], KN [auth j], LI [auth h], LK [auth l], LN [auth j], MI [auth h], NE [auth J], NK [auth l], PM [auth i], QM [auth i], RM [auth i], SH [auth b], SJ [auth e], SP [auth n], TH [auth b], TJ [auth e], TM [auth i], TP [auth n], UJ [auth e], UO [auth g], UP [auth n], VO [auth g], WH [auth b], WJ [auth e], WM [auth i], WO [auth g], WP [auth n], XL [auth f], YL [auth f], YO [auth g], ZG [auth a], ZL [auth f]	(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol C40 H52 O2 DVICWXUADSCSLL-DDEWRDOISA-N
IHT	AM [auth f], CH [auth a], DF [auth O], EJ [auth m], EP [auth R], GL [auth k], HG [auth c], MN [auth j], UH [auth b], VH [auth b], VP [auth n], XO [auth g]	(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol C40 H54 O UNJKJDIRJWIHLL-BQLQDKTLSA-N
WVN	AE [auth B], BE [auth B], BP [auth R], CP [auth R], GE [auth F], HE [auth F], HF [auth K], JE [auth I], JF [auth K], JI [auth h], KE [auth J], LE [auth J], MK [auth l], OF [auth s], QE [auth L], QF [auth s], SM [auth i], UE [auth L], VB [auth A], VE [auth L], VJ [auth e], WB [auth A], XB [auth A], XD [auth B], YB [auth A], YD [auth B], YJ [auth l], ZD [auth B], ZE [auth M]	1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene C40 H56 ANVAOWXLWRTKGA-NTXLUARGSA-N
LMU	DM [auth i]	DODECYL-ALPHA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-YHBSTRCHSA-N
LMT	AC [auth A], FH [auth a], NG [auth a], XH [auth b]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN	SB [auth A], VD [auth B]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4	CE [auth C], DC [auth A], DE [auth C]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Zhang, S.M., Si, L., Li, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--
National Basic Research Program of China (973 Program)	China	--

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary