8XLP

Structure of inactive Photosystem II associated with CAC antenna from Rhodomonas Salina

• PDB DOI: https://doi.org/10.2210/pdb8XLP/pdb
• EM Map EMD-38455: EMDB EMDataResource

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


• Deposited: 2023-12-26 Released: 2024-07-31 
• Deposition Author(s): Si, L., Li, M.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.57 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of inactive Photosystem II associated with CAC antenna from Rhodomonas Salina

Si, L., Li, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 46-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V2W2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 46-mer - A12B10C4D4E2F2G2H2I2J2K2L2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,134.95 kDa 
• Atom Count: 70,547 
• Modelled Residue Count: 6,652 
• Deposited Residue Count: 7,794 
• Unique protein chains: 23

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1	A [auth a], R [auth A]	328	Rhodomonas salina	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for A6MVT2 (Rhodomonas salina) Explore A6MVT2  Go to UniProtKB:  A6MVT2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	B [auth b], S [auth B]	509	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MW31 (Rhodomonas salina) Explore A6MW31  Go to UniProtKB:  A6MW31

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 reaction center protein	C [auth c], T [auth C]	487	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVR2 (Rhodomonas salina) Explore A6MVR2  Go to UniProtKB:  A6MVR2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	D [auth d], U [auth D]	351	Rhodomonas salina	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for A6MVR3 (Rhodomonas salina) Explore A6MVR3  Go to UniProtKB:  A6MVR3

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E [auth e], V [auth E]	84	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVV5 (Rhodomonas salina) Explore A6MVV5  Go to UniProtKB:  A6MVV5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	F [auth f], W [auth F]	42	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVV4 (Rhodomonas salina) Explore A6MVV4  Go to UniProtKB:  A6MVV4

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	G [auth h], X [auth H]	67	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MW35 (Rhodomonas salina) Explore A6MW35  Go to UniProtKB:  A6MW35

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	H [auth i], Y [auth I]	38	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVW0 (Rhodomonas salina) Explore A6MVW0  Go to UniProtKB:  A6MVW0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	I [auth k], Z [auth K]	45	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVZ3 (Rhodomonas salina) Explore A6MVZ3  Go to UniProtKB:  A6MVZ3

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	AA [auth L], J [auth l]	38	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVV3 (Rhodomonas salina) Explore A6MVV3  Go to UniProtKB:  A6MVV3

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein M	BA [auth M], K [auth m]	40	Rhodomonas salina	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	CA [auth T], L [auth t]	32	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MW32 (Rhodomonas salina) Explore A6MW32  Go to UniProtKB:  A6MW32

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein W	DA [auth W], M [auth w]	74	Rhodomonas salina	Mutation(s): 0

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center X protein	EA [auth X], N [auth x]	39	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVU5 (Rhodomonas salina) Explore A6MVU5  Go to UniProtKB:  A6MVU5

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Psb30	FA [auth Y], O [auth y]	34	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVU9 (Rhodomonas salina) Explore A6MVU9  Go to UniProtKB:  A6MVU9

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	GA [auth Z], P [auth z]	62	Rhodomonas salina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A6MVZ2 (Rhodomonas salina) Explore A6MVZ2  Go to UniProtKB:  A6MVZ2

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
NCP	MA [auth G], Q [auth g]	284	Rhodomonas salina	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
CAC2	HA [auth 2], OA [auth O]	217	Rhodomonas salina	Mutation(s): 0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
CAC3	IA [auth 3], PA [auth P]	221	Rhodomonas salina	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
CAC4	JA [auth 4], QA [auth Q]	216	Rhodomonas salina	Mutation(s): 0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
CAC5	KA [auth 5], RA [auth R]	229	Rhodomonas salina	Mutation(s): 0

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
CAC6	LA [auth 6], SA [auth S]	227	Rhodomonas salina	Mutation(s): 0

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
CAC1	NA [auth 1], TA [auth N]	233	Rhodomonas salina	Mutation(s): 0

Small Molecules

Ligands 16 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	IG [auth H], JD [auth h], TF [auth C], UC [auth c]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AD [auth d], AG [auth D], AH [auth 2], AI [auth 4], AK [auth G], AL [auth O], AN [auth R], AO [auth S], BD [auth d], BI [auth 4], BJ [auth 5], BK [auth G], BL [auth O], BN [auth R], CJ [auth 5], CL [auth O], CN [auth R], DF [auth C], DI [auth 4], DK [auth 1], DL [auth O], DN [auth R], EC [auth c], EF [auth C], EI [auth 4], EK [auth 1], EL [auth O], EN [auth R], FC [auth c], FF [auth C], FI [auth 4], FK [auth 1], FN [auth R], GC [auth c], GF [auth C], GI [auth 4], GK [auth 1], GL [auth O], GM [auth Q], GN [auth R], HC [auth c], HE [auth B], HF [auth C], HL [auth O], HM [auth Q], HO [auth N], IB [auth b], IC [auth c], IE [auth B], IF [auth C], IH [auth 3], IK [auth 1], IM [auth Q], IN [auth R], IO [auth N], JB [auth b], JC [auth c], JE [auth B], JF [auth C], JH [auth 3], JI [auth 4], JJ [auth 6], JK [auth 1], JN [auth R], JO [auth N], KB [auth b], KC [auth c], KE [auth B], KF [auth C], KH [auth 3], KI [auth 4], KJ [auth 6], KK [auth 1], KM [auth Q], KO [auth N], LB [auth b], LC [auth c], LE [auth B], LF [auth C], LH [auth 3], LJ [auth 6], LK [auth 1], LM [auth Q], MB [auth b], MC [auth c], ME [auth B], MF [auth C], MJ [auth 6], MM [auth Q], MO [auth N], NB [auth b], NC [auth c], NE [auth B], NF [auth C], NH [auth 3], NM [auth Q], NO [auth N], OB [auth b], OC [auth c], OE [auth B], OF [auth C], OH [auth 3], OJ [auth 6], OO [auth N], PB [auth b], PC [auth c], PE [auth B], PF [auth C], PG [auth 2], PH [auth 3], PJ [auth 6], PK [auth 1], PL [auth P], PO [auth N], QB [auth b], QC [auth c], QD [auth g], QE [auth B], QG [auth 2], QH [auth 3], QJ [auth 6], QK [auth 1], QL [auth P], QM [auth Q], QN [auth S], RB [auth b], RD [auth g], RE [auth B], RG [auth 2], RH [auth 3], RI [auth 5], RL [auth P], RM [auth Q], RN [auth S], SB [auth b], SE [auth B], SG [auth 2], SH [auth 3], SI [auth 5], SJ [auth 6], SL [auth P], SN [auth S], TB [auth b], TE [auth B], TG [auth 2], TI [auth 5], TJ [auth 6], TN [auth S], TO [auth N], UB [auth b], UD [auth A], UE [auth B], UG [auth 2], UI [auth 5], UL [auth P], UO [auth N], VA [auth a], VB [auth b], VD [auth A], VE [auth B], VG [auth 2], VI [auth 5], VL [auth P], VN [auth S], WA [auth a], WB [auth b], WE [auth B], WF [auth D], WG [auth 2], WI [auth 5], WK [auth O], WL [auth P], WN [auth S], XB [auth b], XC [auth d], XD [auth A], XG [auth 2], XI [auth 5], XK [auth O], XL [auth P], XN [auth S], YA [auth a], YI [auth 5], YK [auth O], YL [auth P], YM [auth R], ZF [auth D], ZG [auth 2], ZH [auth 4], ZI [auth 5], ZK [auth O], ZL [auth P], ZM [auth R], ZN [auth S]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	WD [auth A], XA [auth a], XF [auth D], YC [auth d]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	AB [auth a], BE [auth A], CB [auth a], ZD [auth A]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	AF [auth B], BC [auth b], CK [auth G], DG [auth D], ED [auth d], GG [auth F], HD [auth f], HH [auth 2], KG [auth M], LD [auth m], LG [auth W], MD [auth w], NG [auth Z], OD [auth z], OL [auth O], QI [auth 4], SD [auth g], VF [auth C], WC [auth c], XM [auth Q], YF [auth D], ZC [auth d]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	AE [auth A], BB [auth a], BG [auth D], CD [auth d]	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE C53 H80 O2 FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG	BF [auth B], CC [auth b], CG [auth D], DD [auth d], DE [auth A], EB [auth a], FM [auth P], GH [auth 2], GO [auth S], IJ [auth 5], JG [auth L], KD [auth l], NL [auth O], OG [auth Z], PD [auth z], PN [auth R], UF [auth C], VC [auth c], YH [auth 3], ZJ [auth 6]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM	FG [auth E], GD [auth e]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
KC2	AJ [auth 5], CI [auth 4], FL [auth O], HI [auth 4], HK [auth 1], HN [auth R], II [auth 4], JM [auth Q], LO [auth N], MH [auth 3], MK [auth 1], NJ [auth 6], NK [auth 1], OK [auth 1], OM [auth Q], PM [auth Q], QO [auth N], RJ [auth 6], RO [auth N], SO [auth N], TL [auth P], UN [auth S], YG [auth 2], YN [auth S]	Chlorophyll c2 C35 H28 Mg N4 O5 QDRBYWCRXZZVLY-QIEHNWLWSA-L
II0	AM [auth P], BH [auth 2], BM [auth P], BO [auth S], CH [auth 2], CM [auth P], CO [auth S], DH [auth 2], DJ [auth 5], DM [auth P], DO [auth S], EH [auth 2], EJ [auth 5], EO [auth S], FJ [auth 5], GJ [auth 5], IL [auth O], JL [auth O], KL [auth O], KN [auth R], LI [auth 4], LL [auth O], LN [auth R], MI [auth 4], MN [auth R], NI [auth 4], NN [auth R], OI [auth 4], RK [auth 1], SK [auth 1], SM [auth Q], TH [auth 3], TK [auth 1], TM [auth Q], UH [auth 3], UJ [auth 6], UK [auth 1], UM [auth Q], VH [auth 3], VJ [auth 6], VM [auth Q], VO [auth N], WH [auth 3], WJ [auth 6], WO [auth N], XJ [auth 6], XO [auth N], YO [auth N]	(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	FH [auth 2], HJ [auth 5], ML [auth O], ON [auth R], PI [auth 4], VK [auth 1], WM [auth Q], ZO [auth N]	(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	AC [auth b], EG [auth D], EM [auth P], FD [auth d], FO [auth S], HG [auth H], ID [auth h], MG [auth Y], ND [auth y], QF [auth C], RC [auth c], RF [auth C], SC [auth c], SF [auth C], TC [auth c], XE [auth B], XH [auth 3], YB [auth b], YD [auth A], YE [auth B], YJ [auth 6], ZA [auth a], ZB [auth b], ZE [auth B]	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
BCT (Subject of Investigation/LOI)	CE [auth A], DB [auth a]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	TD [auth A], UA [auth a]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
MN	FE [auth A], GB [auth a], GE [auth A], HB [auth a]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	CF [auth C], DC [auth c], EE [auth A], FB [auth a]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.57 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Si, L., Li, M.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	--

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release