8XR6

Cryo-EM structure of cryptophyte photosystem II

• PDB DOI: https://doi.org/10.2210/pdb8XR6/pdb
• EM Map EMD-38596: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Chroomonas placoidea
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-01-06 Released: 2024-06-19 
• Deposition Author(s): Li, K., Zhao, L.S., Zhang, Y.Z., Liu, L.N.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.53 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of cryptophyte photosystem II

Li, K., Zhao, L.S., Zhang, Y.Z., Liu, L.N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 56-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V2W2X2Y2Z2a2b2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 56-mer - A12B7C7D4E2F2G2H2I2J2K2L2M2N2O2P2Q1R1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,325.07 kDa 
• Atom Count: 82,310 
• Modelled Residue Count: 8,208 
• Deposited Residue Count: 9,442 
• Unique protein chains: 28

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II protein D1	A [auth a], B [auth A]	360	Chroomonas placoidea	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for A0A222AI41 (Chroomonas placoidea) Explore A0A222AI41  Go to UniProtKB:  A0A222AI41

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPII-4	C [auth 0], G [auth 4]	219	Chroomonas placoidea	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPII-1	D [auth 1], J [auth 7]	218	Chroomonas placoidea	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPII-2	E [auth 2], K [auth 8]	200	Chroomonas placoidea	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPII-3	F [auth 3], L [auth 9]	229	Chroomonas placoidea	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPII-5	H [auth 5], MA [auth g]	216	Chroomonas placoidea	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPII-6	I [auth 6], VA [auth p]	234	Chroomonas placoidea	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP47 reaction center protein	HA [auth b], M [auth B]	509	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AIE3 (Chroomonas placoidea) Explore A0A222AIE3  Go to UniProtKB:  A0A222AIE3

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbC_CP43	IA [auth c], N [auth C]	473	Chroomonas placoidea	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	JA [auth d], O [auth D]	351	Chroomonas placoidea	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for A0A222AI37 (Chroomonas placoidea) Explore A0A222AI37  Go to UniProtKB:  A0A222AI37

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	KA [auth e], P [auth E]	84	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AI74 (Chroomonas placoidea) Explore A0A222AI74  Go to UniProtKB:  A0A222AI74

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	LA [auth f], Q [auth F]	42	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AI51 (Chroomonas placoidea) Explore A0A222AI51  Go to UniProtKB:  A0A222AI51

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	NA [auth h], R [auth H]	67	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AIE4 (Chroomonas placoidea) Explore A0A222AIE4  Go to UniProtKB:  A0A222AIE4

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	OA [auth i], S [auth I]	38	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AI80 (Chroomonas placoidea) Explore A0A222AI80  Go to UniProtKB:  A0A222AI80

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	PA [auth j], T [auth J]	39	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AI54 (Chroomonas placoidea) Explore A0A222AI54  Go to UniProtKB:  A0A222AI54

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	QA [auth k], U [auth K]	45	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AIA0 (Chroomonas placoidea) Explore A0A222AIA0  Go to UniProtKB:  A0A222AIA0

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	RA [auth l], V [auth L]	38	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AI58 (Chroomonas placoidea) Explore A0A222AI58  Go to UniProtKB:  A0A222AI58

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbM	SA [auth m], W [auth M]	37	Chroomonas placoidea	Mutation(s): 0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Psb-gama_linker	TA [auth n], X [auth N]	297	Chroomonas placoidea	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbO	UA [auth o], Y [auth O]	300	Chroomonas placoidea	Mutation(s): 0

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbQ	WA [auth q], Z [auth Q]	144	Chroomonas placoidea	Mutation(s): 0

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	AA [auth T], XA [auth t]	32	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AID2 (Chroomonas placoidea) Explore A0A222AID2  Go to UniProtKB:  A0A222AID2

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbU	BA [auth U], YA [auth u]	121	Chroomonas placoidea	Mutation(s): 0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II cytochrome c550	CA [auth V], ZA [auth v]	163	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AI35 (Chroomonas placoidea) Explore A0A222AI35  Go to UniProtKB:  A0A222AI35

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
PsbW	AB [auth w], DA [auth W]	130	Chroomonas placoidea	Mutation(s): 0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein X	BB [auth x], EA [auth X]	39	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AI61 (Chroomonas placoidea) Explore A0A222AI61  Go to UniProtKB:  A0A222AI61

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Psb30	CB [auth y], FA [auth Y]	34	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AI69 (Chroomonas placoidea) Explore A0A222AI69  Go to UniProtKB:  A0A222AI69

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	DB [auth z], GA [auth Z]	62	Chroomonas placoidea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A222AI96 (Chroomonas placoidea) Explore A0A222AI96  Go to UniProtKB:  A0A222AI96

Small Molecules

Ligands 16 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	BL [auth H], FN [auth c], GN [auth c], IN [auth c], LO [auth h], MK [auth C], NK [auth C], PK [auth C]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)	AD [auth 1], AF [auth 4], AH [auth 7], AJ [auth B], AK [auth C], AM [auth b], AN [auth c], AO [auth g], AP [auth p], BC [auth A], BD [auth 1], BE [auth 3], BF [auth 4], BG [auth 5], BH [auth 7], BJ [auth B], BK [auth C], BM [auth b], BN [auth c], BO [auth g], BP [auth p], CC [auth 0], CE [auth 3], CF [auth 4], CH [auth 7], CJ [auth B], CK [auth C], CM [auth b], CP [auth p], DC [auth 0], DE [auth 3], DF [auth 4], DG [auth 6], DH [auth 7], DI [auth 9], DJ [auth B], DK [auth C], DM [auth b], DO [auth g], DP [auth p], EC [auth 0], EE [auth 3], EF [auth 4], EG [auth 6], EI [auth 9], EJ [auth B], EK [auth C], EM [auth b], EO [auth g], EP [auth p], FC [auth 0], FE [auth 3], FG [auth 6], FI [auth 9], FJ [auth B], FK [auth C], FL [auth N], FM [auth b], FP [auth p], GE [auth 3], GG [auth 6], GI [auth 9], GJ [auth B], GK [auth C], GL [auth N], GM [auth b], GP [auth p], HC [auth 0], HE [auth 3], HG [auth 6], HI [auth 9], HJ [auth B], HK [auth C], HL [auth N], HM [auth b], IB [auth a], IC [auth 0], IE [auth 3], IG [auth 6], II [auth 9], IJ [auth B], IK [auth C], IL [auth N], IP [auth p], JB [auth a], JC [auth 0], JG [auth 6], JI [auth 9], JJ [auth B], JL [auth N], JP [auth p], KC [auth 0], KD [auth 2], KE [auth 3], KG [auth 6], KI [auth 9], KJ [auth B], KL [auth N], KO [auth g], LB [auth a], LC [auth 0], LD [auth 2], LE [auth 3], LF [auth 5], LG [auth 6], LJ [auth B], LL [auth N], MC [auth 0], MD [auth 2], ME [auth 3], MF [auth 5], MH [auth 8], MI [auth 9], MJ [auth B], MN [auth d], ND [auth 2], NE [auth 3], NF [auth 5], NG [auth 6], NH [auth 8], NI [auth 9], NJ [auth B], NN [auth d], OD [auth 2], OF [auth 5], OG [auth 6], OH [auth 8], OI [auth 9], OJ [auth B], PB [auth a], PD [auth 2], PF [auth 5], PH [auth 8], PI [auth 9], PM [auth c], PP [auth p], QD [auth 2], QF [auth 5], QH [auth 8], QM [auth c], RD [auth 2], RF [auth 5], RH [auth 8], RL [auth b], RM [auth c], RO [auth n], SF [auth 5], SH [auth 8], SL [auth b], SM [auth c], SO [auth n], TC [auth 1], TD [auth 2], TH [auth 8], TK [auth D], TL [auth b], TM [auth c], TO [auth n], UB [auth A], UC [auth 1], UF [auth 5], UG [auth 6], UK [auth D], UL [auth b], UM [auth c], UN [auth g], UO [auth n], VB [auth A], VC [auth 1], VE [auth 4], VF [auth 5], VG [auth 7], VH [auth 8], VL [auth b], VM [auth c], VN [auth g], VO [auth n], WC [auth 1], WE [auth 4], WG [auth 7], WJ [auth C], WL [auth b], WM [auth c], WN [auth g], WO [auth n], XB [auth A], XC [auth 1], XE [auth 4], XG [auth 7], XJ [auth C], XL [auth b], XM [auth c], XN [auth g], YC [auth 1], YE [auth 4], YG [auth 7], YI [auth B], YJ [auth C], YL [auth b], YM [auth c], YN [auth g], YO [auth p], ZC [auth 1], ZG [auth 7], ZI [auth B], ZJ [auth C], ZL [auth b], ZM [auth c], ZN [auth g], ZO [auth p]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	KB [auth a], LN [auth d], SK [auth D], WB [auth A]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	DL [auth J], EL [auth L], NO [auth j], OM [auth c], OO [auth l], QL [auth b], VJ [auth C], XI [auth B]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	HN [auth c], LM [auth b], ML [auth T], NM [auth b], OK [auth C], OL [auth W], PO [auth l], QO [auth m], QP [auth t], RN [auth d], SJ [auth B], SN [auth d], SP [auth w], UJ [auth B], YK [auth D], ZK [auth D]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	NB [auth a], PN [auth d], WK [auth D], ZB [auth A]	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	AC [auth A], AE [auth 3], AG [auth 5], AI [auth 8], CI [auth 9], JD [auth 1], JN [auth d], JO [auth g], KF [auth 4], KN [auth d], LH [auth 7], MM [auth b], OB [auth a], QK [auth D], QN [auth d], RK [auth D], SC [auth 0], TE [auth 3], TJ [auth B], UE [auth 3], VI [auth 9], WI [auth 9], XK [auth D], YD [auth 2]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM	AL [auth F], NL [auth V], RP [auth v], TN [auth f]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
KC2 (Subject of Investigation/LOI)	CD [auth 1], CO [auth g], DD [auth 1], EH [auth 7], FH [auth 7], GC [auth 0], HP [auth p], JE [auth 3], LI [auth 9], MG [auth 6], SD [auth 2], TF [auth 5], UH [auth 8], ZE [auth 4]	Chlorophyll c2 C35 H28 Mg N4 O5 QDRBYWCRXZZVLY-QIEHNWLWSA-L
II0	BI [auth 9], CG [auth 6], FD [auth 1], FO [auth g], GD [auth 1], GF [auth 4], GO [auth g], HD [auth 1], HF [auth 4], HH [auth 7], HO [auth g], ID [auth 1], IF [auth 4], IH [auth 7], JF [auth 4], JH [auth 7], KH [auth 7], KP [auth p], LP [auth p], MP [auth p], NP [auth p], OC [auth 0], OE [auth 3], PC [auth 0], PE [auth 3], PG [auth 6], QC [auth 0], QE [auth 3], QG [auth 6], QI [auth 9], RC [auth 0], RE [auth 3], RG [auth 6], RI [auth 9], SG [auth 6], SI [auth 9], TI [auth 9], UD [auth 2], VD [auth 2], WD [auth 2], WF [auth 5], WH [auth 8], XF [auth 5], XH [auth 8], XO [auth p], YF [auth 5], YH [auth 8], ZD [auth 3]	(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	IO [auth g], OP [auth p], SE [auth 3], TG [auth 6], UI [auth 9], XD [auth 2], ZF [auth 5], ZH [auth 8]	(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
8CT	CL [auth H], CN [auth c], DN [auth c], ED [auth 1], EN [auth c], FF [auth 4], GH [auth 7], IM [auth b], JK [auth C], JM [auth b], KK [auth C], KM [auth b], LK [auth C], MB [auth a], MO [auth h], NC [auth 0], ON [auth d], PJ [auth B], PL [auth Y], QJ [auth B], RJ [auth B], TP [auth y], VK [auth D], YB [auth A]	(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene C40 H56 ANVAOWXLWRTKGA-GZSHKXEASA-N
OEX	EB [auth a], QB [auth A]	CA-MN4-O5 CLUSTER Ca Mn4 O5 SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT	GB [auth a], SB [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	FB [auth a], RB [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	HB [auth a], TB [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.53 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Li, K., Zhao, L.S., Zhang, Y.Z., Liu, L.N.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release