7BGI

Photosystem I of a temperature sensitive mutant Chlamydomonas reinhardtii

• PDB DOI: https://doi.org/10.2210/pdb7BGI/pdb
• EM Map EMD-12180: EMDB EMDataResource

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


• Deposited: 2021-01-07 Released: 2021-12-08 
• Deposition Author(s): Caspy, I., Nelson, N.
• Funding Organization(s): Israel Science Foundation, German-Israeli Foundation for Research and Development

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Dimeric and high-resolution structures of Chlamydomonas Photosystem I from a temperature-sensitive Photosystem II mutant

Caspy, I., Schwartz, T., Bayro-Kaiser, V., Fadeeva, M., Kessel, A., Ben-Tal, N., Nelson, N.

(2021) Commun Biol 4: 1380

• DOI: https://doi.org/10.1038/s42003-021-02911-7

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 21-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 21-mer - A10B2C2D1E1F1G1H1I1J1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 759.85 kDa 
• Atom Count: 52,213 
• Modelled Residue Count: 4,370 
• Deposited Residue Count: 4,399 
• Unique protein chains: 20

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A	741	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
Photosystem I P700 chlorophyll a apoprotein A2	B	733	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
Photosystem I iron-sulfur center	C	80	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
Photosystem I reaction center subunit II, chloroplastic	D	144	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
Photosystem I reaction center subunit IV, chloroplastic	E	63	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
Photosystem I reaction center subunit III, chloroplastic	F	165	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
Photosystem I reaction center subunit V, chloroplastic	G	91	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
Photosystem I reaction center subunit VIII	H [auth I]	37	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A8IFG7 (Chlamydomonas reinhardtii) Explore A8IFG7  Go to UniProtKB:  A8IFG7

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	I [auth J]	39	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P59777 (Chlamydomonas reinhardtii) Explore P59777  Go to UniProtKB:  P59777

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit psaK, chloroplastic	J [auth K]	84	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P14225 (Chlamydomonas reinhardtii) Explore P14225  Go to UniProtKB:  P14225

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
PSI subunit V	K [auth L]	138	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A8IL32 (Chlamydomonas reinhardtii) Explore A8IL32  Go to UniProtKB:  A8IL32

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	L [auth 1], M [auth Z]	194	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q05093 (Chlamydomonas reinhardtii) Explore Q05093  Go to UniProtKB:  Q05093

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	N [auth 3]	219	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q75VY9 (Chlamydomonas reinhardtii) Explore Q75VY9  Go to UniProtKB:  Q75VY9

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	O [auth 7]	213	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q84Y02 (Chlamydomonas reinhardtii) Explore Q84Y02  Go to UniProtKB:  Q84Y02

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	P [auth 8]	217	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q75VY7 (Chlamydomonas reinhardtii) Explore Q75VY7  Go to UniProtKB:  Q75VY7

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	Q [auth 4]	210	Chlamydomonas reinhardtii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q75VZ0 (Chlamydomonas reinhardtii) Explore Q75VZ0  Go to UniProtKB:  Q75VZ0

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	R [auth 5]	227	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q75VY8 (Chlamydomonas reinhardtii) Explore Q75VY8  Go to UniProtKB:  Q75VY8

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	S [auth 6]	229	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for Q75VY6 (Chlamydomonas reinhardtii) Explore Q75VY6  Go to UniProtKB:  Q75VY6

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	T [auth 2]	198	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8IKC8 (Chlamydomonas reinhardtii) Explore A8IKC8  Go to UniProtKB:  A8IKC8

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a-b binding protein, chloroplastic	U [auth 9]	183	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8ITV3 (Chlamydomonas reinhardtii) Explore A8ITV3  Go to UniProtKB:  A8ITV3

Small Molecules

Ligands 25 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	CE [auth B]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL	AL [auth 5], BG [auth 1], BK [auth 4], CJ [auth 8], DI [auth 7], FJ [auth 8], FN [auth 9], HN [auth 9], KH [auth 3], MM [auth 2], NM [auth 2], OG [auth Z], PM [auth 2], RG [auth Z], SL [auth 6], TL [auth 6], UF [auth 1], UG [auth Z], VK [auth 5], VL [auth 6], WJ [auth 4], WK [auth 5], XJ [auth 4], XL [auth 6], ZJ [auth 4]	CHLOROPHYLL B C55 H70 Mg N4 O6 MWVCRINOIIOUAU-UYSPMESUSA-M
CLA	AA [auth A], AB [auth A], AD [auth B], AF [auth K], AI [auth 7], AJ [auth 8], AK [auth 4], AN [auth 9], BA [auth A], BB [auth A], BD [auth B], BF [auth K], BH [auth 3], BI [auth 7], BJ [auth 8], BL [auth 5], BN [auth 9], CA [auth A], CB [auth A], CC [auth B], CD [auth B], CH [auth 3], CI [auth 7], CL [auth 5], CN [auth 9], DA [auth A], DB [auth A], DC [auth B], DD [auth B], DH [auth 3], DJ [auth 8], DN [auth 9], EA [auth A], EB [auth A], EC [auth B], ED [auth B], EH [auth 3], EI [auth 7], EJ [auth 8], EM [auth 2], EN [auth 9], FA [auth A], FB [auth A], FC [auth B], FD [auth B], FF [auth L], FH [auth 3], FI [auth 7], FK [auth 4], FL [auth 6], FM [auth 2], GA [auth A], GB [auth A], GC [auth B], GD [auth B], GF [auth L], GG [auth Z], GH [auth 3], GI [auth 7], GJ [auth 8], GL [auth 6], GM [auth 2], GN [auth 9], HA [auth A], HB [auth A], HC [auth B], HD [auth B], HG [auth Z], HH [auth 3], HI [auth 7], HM [auth 2], IA [auth A], IB [auth A], IC [auth B], ID [auth B], IG [auth Z], IH [auth 3], IM [auth 2], JA [auth A], JB [auth A], JC [auth B], JD [auth B], JG [auth Z], JH [auth 3], JM [auth 2], KA [auth A], KC [auth B], KD [auth B], KG [auth Z], KM [auth 2], LA [auth A], LC [auth B], LD [auth B], LE [auth F], LG [auth Z], LH [auth 3], LL [auth 6], LM [auth 2], MA [auth A], MC [auth B], MD [auth B], ME [auth F], MF [auth 1], MG [auth Z], MH [auth 3], MK [auth 5], ML [auth 6], NA [auth A], NC [auth B], ND [auth B], NF [auth 1], NG [auth Z], NH [auth 3], NK [auth 5], NL [auth 6], OA [auth A], OC [auth B], OD [auth B], OF [auth 1], OI [auth 7], OJ [auth 4], OK [auth 5], OL [auth 6], OM [auth 2], PA [auth A], PC [auth B], PD [auth B], PE [auth G], PF [auth 1], PG [auth Z], PI [auth 8], PJ [auth 4], PK [auth 5], PL [auth 6], QA [auth A], QC [auth B], QD [auth B], QE [auth G], QF [auth 1], QG [auth Z], QH [auth 3], QI [auth 8], QJ [auth 4], QK [auth 5], QL [auth 6], QM [auth 2], RA [auth A], RC [auth B], RD [auth B], RF [auth 1], RH [auth 7], RJ [auth 4], RK [auth 5], RL [auth 6], SA [auth A], SC [auth B], SD [auth B], SF [auth 1], SG [auth Z], SJ [auth 4], SK [auth 5], TA [auth A], TC [auth B], TE [auth J], TF [auth 1], TJ [auth 4], TK [auth 5], UA [auth A], UC [auth B], UJ [auth 4], UK [auth 5], UL [auth 6], VA [auth A], VC [auth B], VF [auth 1], VH [auth 7], VI [auth 8], VJ [auth 4], W [auth A], WA [auth A], WB [auth A], WC [auth B], WF [auth 1], WH [auth 7], WI [auth 8], WL [auth 6], WM [auth 9], X [auth A], XA [auth A], XB [auth A], XC [auth B], XF [auth 1], XH [auth 7], XI [auth 8], XK [auth 5], XM [auth 9], Y [auth A], YA [auth A], YB [auth A], YC [auth B], YE [auth K], YF [auth 1], YH [auth 7], YI [auth 8], YJ [auth 4], YK [auth 5], YL [auth 6], YM [auth 9], Z [auth A], ZA [auth A], ZC [auth B], ZE [auth K], ZH [auth 7], ZI [auth 8], ZK [auth 5], ZL [auth 6], ZM [auth 9]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0	V [auth A]	CHLOROPHYLL A ISOMER C55 H72 Mg N4 O5 VIQFHHZSLDFWDU-DVXFRRMCSA-M
T7X	HE [auth B]	Phosphatidylinositol C47 H83 O13 P KRTOMQDUKGRFDJ-TWUHCGEESA-N
SQD	AG [auth 1], TM [auth 2]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	AC [auth A], WE [auth J]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	AE [auth B], BE [auth B], CK [auth 4], DK [auth 4], DL [auth 5], EE [auth B], HJ [auth 8], HL [auth 6], II [auth 7], IN [auth 9], OH [auth 3], RB [auth A], RM [auth 2], SB [auth A], TG [auth Z], ZF [auth 1]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH	AM [auth 6], GK [auth 5], JI [auth 7], RI [auth 8], SM [auth 2]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C39 H77 O8 P YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA	BC [auth A], JN [auth 9]	DIACYL GLYCEROL C39 H76 O5 UHUSDOQQWJGJQS-QNGWXLTQSA-N
LUT	BM [auth 2], CG [auth Z], CM [auth 2], DG [auth Z], DM [auth 2], EG [auth Z], HK [auth 5], IK [auth 5], IL [auth 6], JF [auth 1], JL [auth 6], KF [auth 1], LJ [auth 4], MJ [auth 4], SH [auth 7], SI [auth 8], TH [auth 7], TI [auth 8], UM [auth 9], VG [auth 3], VM [auth 9], WG [auth 3]	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL C40 H56 O2 KBPHJBAIARWVSC-NSIPBSJQSA-N
C7Z	LF [auth 1], LK [auth 5], VE [auth J]	(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol C40 H56 O2 JKQXZKUSFCKOGQ-ANDPMPNWSA-N
RRX	NE [auth F]	(3R)-beta,beta-caroten-3-ol C40 H56 O DMASLKHVQRHNES-FKKUPVFPSA-N
BCR	AH [auth 3], CF [auth K], EF [auth L], EL [auth 6], GE [auth B], HF [auth L], JK [auth 5], KK [auth 5], KL [auth 6], MB [auth A], MI [auth 7], NB [auth A], NJ [auth 4], OB [auth A], PB [auth A], QB [auth A], RE [auth G], SE [auth I], UD [auth B], UE [auth J], UH [auth 7], UI [auth 8], VD [auth B], WD [auth B], XD [auth B], XE [auth K], XG [auth 3], YD [auth B], YG [auth 3], ZD [auth B], ZG [auth 3]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	DE [auth B], EK [auth 4], IE [auth B], IF [auth 1], KJ [auth 8], KN [auth 9], OE [auth F], UB [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
LPX	JJ [auth 8]	(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate C21 H44 N O7 P YVYMBNSKXOXSKW-FQEVSTJZSA-N
PQN	KB [auth A], TD [auth B]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
NKP	IJ [auth 8], PH [auth 3], TB [auth A]	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate C21 H41 O7 P WRGQSWVCFNIUNZ-SQUSKLHYSA-N
SF4	JE [auth C], KE [auth C], LB [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
SPH	DF [auth K], KI [auth 7], NI [auth 7]	SPHINGOSINE C18 H37 N O2 WWUZIQQURGPMPG-MSOLQXFVSA-N
QTB	FG [auth Z]	(3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one C18 H28 O WXNCHUZBWWHNPM-FHRFKLSGSA-N
PLM	LI [auth 7]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
DAO	ZB [auth A]	LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N
OCA	VB [auth A]	OCTANOIC ACID (CAPRYLIC ACID) C8 H16 O2 WWZKQHOCKIZLMA-UHFFFAOYSA-N
CA	FE [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNC	D	L-PEPTIDE LINKING	C3 H6 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0.7
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-08 
Deposition Author(s): Caspy, I., Nelson, N.

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Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	569/17
German-Israeli Foundation for Research and Development	Israel	G-1483-207/2018

Revision History  

• Version 1.0: 2021-12-08
  Type: Initial release
  
• Version 1.1: 2021-12-15
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Refinement description, Structure summary