6IJO

Photosystem I of Chlamydomonas reinhardtii

• PDB DOI: https://doi.org/10.2210/pdb6IJO/pdb
• EM Map EMD-9680: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Chlamydomonas reinhardtii
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-10-10 Released: 2019-03-20 
• Deposition Author(s): Pan, X., Ma, J., Su, X., Liu, Z., Zhang, X., Li, M.
• Funding Organization(s): Ministry of Science and Technology (China), Chinese Academy of Sciences, National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Antenna arrangement and energy transfer pathways of a green algal photosystem-I-LHCI supercomplex.

Su, X., Ma, J., Pan, X., Zhao, X., Chang, W., Liu, Z., Zhang, X., Li, M.

(2019) Nat Plants 5: 273-281

• PubMed: 30850819 
• DOI: https://doi.org/10.1038/s41477-019-0380-5
• Primary Citation of Related Structures:  
  6IJJ, 6IJO


• PubMed Abstract: 
  

  During oxygenic photosynthesis, photosystems I and II (PSI and PSII) are essential for light-driven electron transport. Excitation energy transfer in PSI occurs extremely quickly, making it an efficient energy converter. In the alga Chlamydomonas reinhardtii (Cr), multiple units of light-harvesting complex I (LHCI) bind to the PSI core and function as peripheral antennae, forming a PSI-LHCI supercomplex. CrPSI-LHCI shows significantly larger antennae compared with plant PSI-LHCI while maintaining highly efficient energy transfer from LHCI to PSI. Here, we report structures of CrPSI-LHCI, solved by cryo-electron microscopy, revealing that up to ten LHCIs are associated with the PSI core. The structures provide detailed information about antenna organization and pigment arrangement within the supercomplexes. Highly populated and closely associated chlorophylls in the antennae explain the high efficiency of light harvesting and excitation energy transfer in CrPSI-LHCI.

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Organizational Affiliation: 

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 23-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 23-mer - A10B2C2D2E1F1G1H1I1J1K1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 892.59 kDa 
• Atom Count: 49,685 
• Modelled Residue Count: 4,382 
• Deposited Residue Count: 5,718 
• Unique protein chains: 22

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaA	A	751	Chlamydomonas reinhardtii	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P12154 (Chlamydomonas reinhardtii) Explore P12154  Go to UniProtKB:  P12154

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaB	B	735	Chlamydomonas reinhardtii	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P09144 (Chlamydomonas reinhardtii) Explore P09144  Go to UniProtKB:  P09144

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaC	C	81	Chlamydomonas reinhardtii	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for Q00914 (Chlamydomonas reinhardtii) Explore Q00914  Go to UniProtKB:  Q00914

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaD	D	247	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q39615 (Chlamydomonas reinhardtii) Explore Q39615  Go to UniProtKB:  Q39615

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaE	E	143	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12352 (Chlamydomonas reinhardtii) Explore P12352  Go to UniProtKB:  P12352

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaF	F	227	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P12356 (Chlamydomonas reinhardtii) Explore P12356  Go to UniProtKB:  P12356

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaG	G	159	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P14224 (Chlamydomonas reinhardtii) Explore P14224  Go to UniProtKB:  P14224

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaH	H	155	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P13352 (Chlamydomonas reinhardtii) Explore P13352  Go to UniProtKB:  P13352

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaI	I	106	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A8IFG7 (Chlamydomonas reinhardtii) Explore A8IFG7  Go to UniProtKB:  A8IFG7

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaJ	J	41	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P59777 (Chlamydomonas reinhardtii) Explore P59777  Go to UniProtKB:  P59777

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaK	K	160	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P14225 (Chlamydomonas reinhardtii) Explore P14225  Go to UniProtKB:  P14225

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaL	L	258	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A8IL32 (Chlamydomonas reinhardtii) Explore A8IL32  Go to UniProtKB:  A8IL32

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Lhca1	M [auth 1], N [auth a]	248	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q05093 (Chlamydomonas reinhardtii) Explore Q05093  Go to UniProtKB:  Q05093

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Lhca3	O [auth 3]	298	Chlamydomonas reinhardtii	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Lhca4	P [auth 4]	290	Chlamydomonas reinhardtii	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Lhca5	Q [auth 5]	274	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q75VY8 (Chlamydomonas reinhardtii) Explore Q75VY8  Go to UniProtKB:  Q75VY8

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Lhca6	R [auth 6]	318	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q75VY6 (Chlamydomonas reinhardtii) Explore Q75VY6  Go to UniProtKB:  Q75VY6

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Lhca7	S [auth 7]	241	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q75VY4 (Chlamydomonas reinhardtii) Explore Q75VY4  Go to UniProtKB:  Q75VY4

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Lhca8	T [auth 8]	272	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q75VY7 (Chlamydomonas reinhardtii) Explore Q75VY7  Go to UniProtKB:  Q75VY7

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Lhca2	U [auth 2]	227	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8IKC8 (Chlamydomonas reinhardtii) Explore A8IKC8  Go to UniProtKB:  A8IKC8

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Lhca9	V [auth 9]	213	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8ITV3 (Chlamydomonas reinhardtii) Explore A8ITV3  Go to UniProtKB:  A8ITV3

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
ChainX	W [auth X]	26	Chlamydomonas reinhardtii	Mutation(s): 0

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	AE [auth B], NE [auth J]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AA [auth A], AB [auth A], AD [auth B], AG [auth a], AK [auth 7], AL [auth 8], BA [auth A], BB [auth A], BD [auth B], BF [auth 1], BG [auth a], BI [auth 5], BJ [auth 6], BK [auth 7], BL [auth 8], CA [auth A], CB [auth A], CD [auth B], CF [auth 1], CG [auth a], CI [auth 5], CJ [auth 6], CK [auth 7], CL [auth 8], DA [auth A], DB [auth A], DD [auth B], DF [auth 1], DG [auth a], DI [auth 5], DJ [auth 6], DK [auth 7], DL [auth 8], DM [auth 9], EA [auth A], EB [auth A], ED [auth B], EE [auth F], EF [auth 1], EG [auth a], EI [auth 5], EJ [auth 6], EK [auth 7], EL [auth 8], EM [auth 9], FA [auth A], FB [auth A], FC [auth B], FD [auth B], FE [auth F], FF [auth 1], FG [auth a], FI [auth 5], FJ [auth 6], FK [auth 7], FL [auth 8], FM [auth 9], GA [auth A], GB [auth A], GC [auth B], GD [auth B], GE [auth F], GF [auth 1], GG [auth a], GH [auth 4], GI [auth 5], GJ [auth 6], GK [auth 7], GM [auth 9], HA [auth A], HB [auth A], HC [auth B], HD [auth B], HF [auth 1], HH [auth 4], HI [auth 5], HJ [auth 6], HK [auth 7], HM [auth 9], IA [auth A], IB [auth A], IC [auth B], ID [auth B], IE [auth G], IF [auth 1], IH [auth 4], II [auth 5], IJ [auth 6], IK [auth 7], IM [auth 9], JA [auth A], JB [auth A], JC [auth B], JD [auth B], JE [auth G], JF [auth 1], JH [auth 4], JI [auth 5], JJ [auth 6], JK [auth 7], JM [auth 9], KA [auth A], KB [auth A], KC [auth B], KD [auth B], KF [auth 1], KH [auth 4], KI [auth 5], KJ [auth 6], KK [auth 7], KM [auth 9], LA [auth A], LB [auth A], LC [auth B], LD [auth B], LE [auth J], LF [auth 1], LG [auth 3], LH [auth 4], LI [auth 5], LJ [auth 6], LK [auth 7], LM [auth 9], MA [auth A], MB [auth A], MC [auth B], MD [auth B], MF [auth 1], MG [auth 3], MH [auth 4], MI [auth 5], MJ [auth 6], MM [auth 9], NA [auth A], NB [auth A], NC [auth B], ND [auth B], NF [auth 1], NG [auth 3], NH [auth 4], NI [auth 5], NJ [auth 6], NL [auth 2], NM [auth 9], OA [auth A], OC [auth B], OD [auth B], OF [auth 1], OG [auth 3], OH [auth 4], OI [auth 5], OJ [auth 6], OL [auth 2], OM [auth 9], PA [auth A], PB [auth A], PC [auth B], PD [auth B], PE [auth K], PG [auth 3], PH [auth 4], PI [auth 5], PJ [auth 6], PL [auth 2], QA [auth A], QC [auth B], QD [auth B], QG [auth 3], QH [auth 4], QI [auth 5], QJ [auth 6], QL [auth 2], RA [auth A], RC [auth B], RD [auth B], RE [auth K], RG [auth 3], RH [auth 4], RI [auth 5], RL [auth 2], SA [auth A], SC [auth B], SD [auth B], SE [auth K], SG [auth 3], SH [auth 4], SJ [auth 6], SK [auth 8], SL [auth 2], TA [auth A], TC [auth B], TE [auth K], TF [auth a], TG [auth 3], TH [auth 4], TK [auth 8], TL [auth 2], UA [auth A], UC [auth B], UF [auth a], UG [auth 3], UH [auth 4], UK [auth 8], UL [auth 2], VA [auth A], VC [auth B], VF [auth a], VG [auth 3], VK [auth 8], VL [auth 2], WA [auth A], WC [auth B], WF [auth a], WG [auth 3], WK [auth 8], WL [auth 2], X [auth A], XA [auth A], XC [auth B], XE [auth L], XF [auth a], XG [auth 3], XJ [auth 7], XK [auth 8], XL [auth 2], Y [auth A], YA [auth A], YB [auth A], YC [auth B], YE [auth L], YF [auth a], YG [auth 3], YJ [auth 7], YK [auth 8], YL [auth 2], Z [auth A], ZA [auth A], ZC [auth B], ZE [auth L], ZF [auth a], ZJ [auth 7], ZK [auth 8], ZL [auth 2]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG	AI [auth 4], DC [auth A], OE [auth J], RK [auth 7], YI [auth 5], ZH [auth 4], ZI [auth 5]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	BE [auth B], CM [auth 2], EH [auth 3], FH [auth 3], JL [auth 8], KG [auth a], KL [auth 8], PK [auth 7], QB [auth A], RB [auth A], RM [auth 9], SF [auth 1], VI [auth 5], VJ [auth 6], XI [auth 5], YH [auth 4]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX	WI [auth 5], WJ [auth 6]	(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL C40 H56 O4 PGYAYSRVSAJXTE-OQASCVKESA-N
XAT	AH [auth 3], BM [auth 2], HL [auth 8], IG [auth a], NK [auth 7], QF [auth 1], QM [auth 9], TI [auth 5], TJ [auth 6], WH [auth 4]	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O4 SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT	AM [auth 2], GL [auth 8], HG [auth a], MK [auth 7], PF [auth 1], PM [auth 9], RJ [auth 6], SI [auth 5], VH [auth 4], ZG [auth 3]	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O2 KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR	AF [auth L], BH [auth 3], CH [auth 3], DH [auth 3], EC [auth B], HE [auth F], IL [auth 8], JG [auth a], KE [auth G], ME [auth J], OK [auth 7], QE [auth K], QK [auth 7], RF [auth 1], SB [auth A], TB [auth A], UB [auth A], UD [auth B], UE [auth K], UI [auth 5], UJ [auth 6], VB [auth A], VD [auth B], WB [auth A], WD [auth B], WE [auth L], XD [auth B], XH [auth 4], YD [auth B], ZB [auth A], ZD [auth B]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMU	AC [auth A], AJ [auth 5], BC [auth A], CC [auth A], LL [auth 8], ML [auth 8], VE [auth K]	DODECYL-ALPHA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN	OB [auth A], TD [auth B]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4	CE [auth C], DE [auth C], XB [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Pan, X., Ma, J., Su, X., Liu, Z., Zhang, X., Li, M.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2017YFA0503702
Ministry of Science and Technology (China)	China	2017YFA0504700
Ministry of Science and Technology (China)	China	2016YFA0502900
Chinese Academy of Sciences	China	XDB08020302
Chinese Academy of Sciences	China	XDB08030204
Chinese Academy of Sciences	China	XDB27020106
Chinese Academy of Sciences	China	QYZDB-SSW-SMC005
National Natural Science Foundation of China	China	31770778
National Natural Science Foundation of China	China	31700649
National Natural Science Foundation of China	China	31600609

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Database references, Structure summary
• Version 2.0: 2019-05-01
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary